dputhier / pygtftk Goto Github PK
View Code? Open in Web Editor NEWA python package and a set of shell commands to handle GTF files
License: GNU General Public License v3.0
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Completion not working under zsh
See the title... No idea at the moment...
For test reproducibility chrom_info_as_dict should use an OrderedDict instead of a defaultDict
TODO
split command
Could be helpful to have a split command.
e.g
gtftk split -k gene_biotype
gtftk split -k chrom
Adding test to check wether bigwigs contain the expected chrs
bw = pyBigWig.open("test/test.bw")
bw.chroms().keys()
peak_anno error upon installation
Got an error during installation of pygtftk (related to cythonization of create_shuffle)
pygtftk/stats/intersect/create_shuffles.c:626:10: fatal error: 'numpy/arrayobject.h' file not found
#include "numpy/arrayobject.h"
^
1 error generated.
error: command 'clang' failed with exit status 1
Closest_gn_to_feat
In case sloped regions exceed genome size the computed distance to the features going outside genome limits could be wrong. Should be extremely rare but should be fixed.
Doc: The gtftk.bam.bam_coverage_matrix module
The title should be related to bwig not bam.
divergent / convergent list of transcript
In the current implementation only a single transcript is added in the "divergent" key. The list of all of them should be returned.
libgtftk.so compilation
from fafa: The pb with compilation of library is still there. When you do a "file" on the library compiled with gtftk installation, you get : Mach-O 64-bit bundle x86_64
The same "file" on the library I compiled by hand ( gcc -o libgtftk.so -fPIC -shared -lz -I. .c command/.c ) give : Mach-O 64-bit dynamically linked shared library x86_64
The right options (-dynamiclib -shared) appears on the compilation lines but not on the link line, when you link together all the compiled files to build the library. It is probably needed to add these options elsewhere in the config file to tell the linker to make a dynamically linked shared library instead of a bundle.
Check whether -C is supported with 'retrieve'
.gtftk versioning
It could be interesting to allow several subdirectories in .gtftk (that would be named according to a hash computed from the path to the gtftk script). The idea would be to avoid collisions between several versions of pygtftk (e.g installed through several envs) with potentially various plugins.
Add a command-wise argument to convert (chr)MT into (chr)M
This is in progress and will be part of the next libgtftk release.
Segfault when using bed3 files
Using peak_anno with a bed3 file triggers a segfault. No other messages are displayed, even with high verbosity.
Command example :
gtftk peak_anno -i hg38.gtf.gz -c hg38_ensembl.genome -p bed3_h3k4me3.bed -V 3
The command works fine the exact same file is converted to a bed6 with filler characters (eg. 'chr1 100 200' becomes 'chr1 100 200 A B C')
I suspect this is related to the argument formatter and could appear in other parts of the pygtftk project.
Bad extension check for outfile in gtftk coverage
It seems that new version of gtftk coverage expects outfile to be a bw whereas it can be a tabulated matrix with --matrix-out.
gtftk coverage --inputfile out/bedtools/merge/bedtools/multiinter_bed-hg38-bs-hypometh-thymus/multiinter.bed --outfile out/gtftk/coverage_chrominfo-hg38-main-chr_upstream-2000_downstream-2000_pseudocount-0_nbwindow-20_nhighest-5_matrixout_bed-hg38-bs-hypometh-thymus-union-all_bw-hg38-H3K27ac-thymus-merged-wiq.txt --chrom-info out/awk/extract_main_chr/gunzip/to-stdout/rsync/ucsc/goldenPath/hg38/database/chromInfo.txt --nb-proc 1 --nb-window 20 --matrix-out --upstream 2000 --downstream 2000 --pseudo-count 0 --n-highest 5 out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/CD34_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/EC_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/LC_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/SP4_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/SP8_qnorVS_SP8.bw
|--- 23:50-WARNING : Not a valid filename extension
|--- 23:50-ERROR : Extension expected: ('\\.[Bb][Ww]$', '\\.[Bb][Ii][Gg][Ww][Ii][Gg]$')Redirecting through stdout avoid extension check and the output file seems to be correct.
gtftk coverage --inputfile out/bedtools/merge/bedtools/multiinter_bed-hg38-bs-hypometh-thymus/multiinter.bed --chrom-info out/awk/extract_main_chr/gunzip/to-stdout/rsync/ucsc/goldenPath/hg38/database/chromInfo.txt --nb-proc 1 --nb-window 20 --matrix-out --upstream 2000 --downstream 2000 --pseudo-count 0 --n-highest 5 out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/CD34_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/EC_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/LC_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/SP4_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/SP8_qnorVS_SP8.bw > debug.txtLibrary is not dynamic
Hello Denis,
I cloned and install this new github repository without problem on blackflag. All is working fine except the library that seems to be not dynamically compiled. Can you check that you compile libgtftk.so with the "-shared" and "-fPIC" options ?
force-tx-class is not supported in profile
Some functions use mutable arguments as default arg
Harmful. Should be fixed.
Improving the detection/annotation of alternative splicing events
It would be interesting to create plugins to detect the various spicing events described in Hadas Keren, Galit Lev-Maor & Gil Ast (Alternative splicing and evolution: diversification, exon definition and function).
http://www.nature.com.gate2.inist.fr/nrg/journal/v11/n5/box/nrg2776_BX1.html
See also:
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-81
peakanno and default chrom size
The use of a proper set of chromosome size is important for user to get the right stats. I would suggest to provide a set of default chromosome size to users at least for common genomes and version (hs, mm, rn, dm...). This could depend on a function implemented in the utils module that would exploit the pybedtools.helpers.chromsizes(genome) and pybedtools.helpers.chromsizes_to_file(…[, fn]).
ERROR-mk_matrix with conda packaged version of release 0.9.1
The first conda package for pygtftk is out:
https://anaconda.org/guillaumecharbonnier/pygtftk
I am not able to pass tests requiring this file though:
ERROR-mk_matrix : Not a bigwig file :pygtftk/data/simple/simple.bw
Maybe an issue with the version of pyBigWig?
bigwig = pyBigWig.open(big_wig)
if not bigwig.isBigWig():
message("Not a bigwig file :" + big_wig, type="ERROR")
Version of pybigwig in packaged environment:
https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.2.8-py27_0.tar.bz2
Version of pybigwig in working unpackaged environment:
https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.3.10-np113py27_0.tar.bz2
Currently rebuilding with higher-version requirement to see if it solves the issue.
ArgFormatter.bed6
Instead of screaming when provided a bed3 file, bed6 should instead automatically convert it to bed6 and display a warning for the user.
Hardcoded gcc at some point in setup.py?
I have been trying for a few days to build pygtftk using bioconda guidelines.
I am not sure about what I am saying but I think that it is failing until now because "gcc" is called somewhere in the install script and the bioconda building environment does not have "gcc". Instead it modifies CC and other C-related variables like this:
echo $CC
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
For the first part of setup.py, everything is fine because compilations are using the "conda gcc":
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/blast_reader.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/blast_reader.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
But then, after a few ones, "gcc" is used instead and fail because it corresponds to nothing in the environment:
gcc -pthread -shared -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -Wl,-rpath=/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib,--no-as-needed -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -Wl,-rpath=/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib,--no-as-needed -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/blast_reader.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attributes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_to_pos.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_blast.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/merge_attr.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_positions.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_column.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_transcript.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_exon_number.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_prefix.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/libgtftk.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_raw_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/column.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_gtf_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_number_of_exon.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/convert_to_ensembl.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/extract_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_genomic_location.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/clear_indexes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_list.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_key.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_sequences.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/globals.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/del_attributes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_gtf.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/gtf_reader.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_transcript_size.o -L/usr/lib -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -lz -lpython3.6m -o build/lib.linux-x86_64-3.6/pygtftk/lib/libgtftk.cpython-36m-x86_64-linux-gnu.so
@dputhier, do you know how to patch setup.py to always use gcc in CC?
Here is the full log:
No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.11
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.11
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Adding in variants from /opt/conda/conda_build_config.yaml
INFO:conda_build.variants:Adding in variants from /opt/conda/conda_build_config.yaml
Adding in variants from /root/project/recipes/pygtftk/conda_build_config.yaml
INFO:conda_build.variants:Adding in variants from /root/project/recipes/pygtftk/conda_build_config.yaml
Adding in variants from /opt/conda/lib/python3.6/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
INFO:conda_build.variants:Adding in variants from /opt/conda/lib/python3.6/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
Attempting to finalize metadata for pygtftk
INFO:conda_build.metadata:Attempting to finalize metadata for pygtftk
Solving environment: ...working... done
Solving environment: ...working... done
Solving environment: ...working... done
BUILD START: ['pygtftk-0.9.7-py36hebb334c_1.tar.bz2']
Solving environment: ...working... done
## Package Plan ##
environment location: /opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place
The following NEW packages will be INSTALLED:
argparse: 1.4.0-py36_0 bioconda
asn1crypto: 0.24.0-py36_1003 conda-forge
bcftools: 1.9-h4da6232_0 bioconda
bedtools: 2.27.1-he941832_2 bioconda
biopython: 1.72-py36_0 conda-forge
blas: 1.1-openblas conda-forge
boost-cpp: 1.67.0-h3a22d5f_0 conda-forge
bzip2: 1.0.6-h470a237_2 conda-forge
ca-certificates: 2018.8.24-ha4d7672_0 conda-forge
cairo: 1.14.12-he6fea26_5 conda-forge
certifi: 2018.8.24-py36_1001 conda-forge
cffi: 1.11.5-py36h5e8e0c9_1 conda-forge
chardet: 3.0.4-py36_1003 conda-forge
click: 7.0-py_0 conda-forge
click-plugins: 1.0.4-py_0 conda-forge
cligj: 0.5.0-py_0 conda-forge
cloudpickle: 0.6.0-py_0 conda-forge
cryptography: 2.3.1-py36hdffb7b8_0 conda-forge
cryptography-vectors: 2.3.1-py36_1000 conda-forge
curl: 7.61.1-h74213dd_2 conda-forge
cycler: 0.10.0-py_1 conda-forge
cython: 0.28.5-py36hfc679d8_0 conda-forge
dbus: 1.13.0-h3a4f0e9_0 conda-forge
descartes: 1.1.0-py_2 conda-forge
expat: 2.2.5-hfc679d8_2 conda-forge
fiona: 1.7.13-py36hb00a9d7_3 conda-forge
fontconfig: 2.13.1-h65d0f4c_0 conda-forge
freetype: 2.9.1-h6debe1e_4 conda-forge
freexl: 1.0.5-h470a237_2 conda-forge
ftputil: 3.4-py_0 conda-forge
future: 0.16.0-py36_1002 conda-forge
gdal: 2.2.4-py36hb00a9d7_9 conda-forge
geopandas: 0.4.0-py_1 conda-forge
geos: 3.6.2-hfc679d8_3 conda-forge
geotiff: 1.4.2-h700e5ad_4 conda-forge
gettext: 0.19.8.1-h5e8e0c9_1 conda-forge
giflib: 5.1.4-h470a237_1 conda-forge
glib: 2.55.0-h464dc38_2 conda-forge
gst-plugins-base: 1.12.5-hde13a9d_0 conda-forge
gstreamer: 1.12.5-h61a6719_0 conda-forge
hdf4: 4.2.13-h951d187_2 conda-forge
hdf5: 1.10.2-hc401514_2 conda-forge
htslib: 1.9-hc238db4_4 bioconda
icu: 58.2-hfc679d8_0 conda-forge
idna: 2.7-py36_1002 conda-forge
jpeg: 9c-h470a237_1 conda-forge
json-c: 0.12.1-h470a237_1 conda-forge
kealib: 1.4.9-h0bee7d0_2 conda-forge
kiwisolver: 1.0.1-py36h2d50403_2 conda-forge
krb5: 1.16.1-hbb41f41_0 conda-forge
libcurl: 7.61.1-hbdb9355_2 conda-forge
libdap4: 3.19.1-h8fe5423_1 conda-forge
libdeflate: 1.0-h470a237_0 bioconda
libedit: 3.1.20170329-haf1bffa_1 conda-forge
libffi: 3.2.1-hfc679d8_5 conda-forge
libgcc-ng: 8.2.0-hdf63c60_1 defaults
libgdal: 2.2.4-hbd6f514_9 conda-forge
libgfortran: 3.0.0-1 conda-forge
libiconv: 1.15-h470a237_3 conda-forge
libkml: 1.3.0-hccc92b1_8 conda-forge
libnetcdf: 4.6.1-he6cff42_8 conda-forge
libpng: 1.6.35-ha92aebf_2 conda-forge
libpq: 10.5-he29860b_0 conda-forge
libspatialindex: 1.8.5-hfc679d8_3 conda-forge
libspatialite: 4.3.0a-hdfcc80b_23 conda-forge
libssh2: 1.8.0-h5b517e9_2 conda-forge
libstdcxx-ng: 7.2.0-hdf63c60_3 conda-forge
libtiff: 4.0.9-he6b73bb_2 conda-forge
libuuid: 2.32.1-h470a237_2 conda-forge
libxcb: 1.13-h470a237_2 conda-forge
libxml2: 2.9.8-h422b904_5 conda-forge
matplotlib: 2.2.3-py36h8e2386c_0 conda-forge
mizani: 0.4.6-py_0 conda-forge
munch: 2.3.2-py_0 conda-forge
ncurses: 6.1-hfc679d8_1 conda-forge
numpy: 1.9.3-py36_blas_openblashd3ea46f_206 conda-forge [blas_openblas]
openblas: 0.2.20-8 conda-forge
openjpeg: 2.3.0-h0e734dc_3 conda-forge
openssl: 1.0.2p-h470a237_0 conda-forge
palettable: 3.1.1-py_0 conda-forge
pandas: 0.23.4-py36hf8a1672_0 conda-forge
patsy: 0.5.0-py_1 conda-forge
pcre: 8.41-hfc679d8_3 conda-forge
pip: 18.1-py36_1000 conda-forge
pixman: 0.34.0-h470a237_3 conda-forge
plotnine: 0.4.0-py_0 conda-forge
poppler: 0.67.0-h4d7e492_3 conda-forge
poppler-data: 0.4.9-0 conda-forge
postgresql: 10.5-h66035e0_0 conda-forge
proj4: 4.9.3-h470a237_8 conda-forge
psycopg2: 2.7.5-py36hdffb7b8_2 conda-forge
pthread-stubs: 0.4-h470a237_1 conda-forge
pybedtools: 0.7.10-py36ha92aebf_3 bioconda
pybigwig: 0.3.12-py36hdfb72b2_0 bioconda
pycparser: 2.19-py_0 conda-forge
pyopenssl: 18.0.0-py36_1000 conda-forge
pyparsing: 2.2.2-py_0 conda-forge
pyproj: 1.9.5.1-py36h508ed2a_5 conda-forge
pyqt: 5.6.0-py36h8210e8a_7 conda-forge
pysal: 1.14.4.post2-py36_1 conda-forge
pysam: 0.15.1-py36h0380709_0 bioconda
pysocks: 1.6.8-py36_1002 conda-forge
python: 3.6.6-h5001a0f_0 conda-forge
python-dateutil: 2.7.3-py_0 conda-forge
pytz: 2018.5-py_0 conda-forge
pyyaml: 3.13-py36h470a237_1 conda-forge
qt: 5.6.2-hf70d934_9 conda-forge
readline: 7.0-haf1bffa_1 conda-forge
requests: 2.19.1-py36_1001 conda-forge
rtree: 0.8.3-py36_1000 conda-forge
samtools: 1.9-h8ee4bcc_1 bioconda
scipy: 1.1.0-py36_blas_openblashd3ea46f_201 conda-forge [blas_openblas]
setuptools: 40.4.3-py36_0 conda-forge
shapely: 1.6.4-py36h164cb2d_1 conda-forge
sip: 4.18.1-py36hfc679d8_0 conda-forge
six: 1.11.0-py36_1001 conda-forge
sqlalchemy: 1.2.12-py36h470a237_0 conda-forge
sqlite: 3.25.2-hb1c47c0_0 conda-forge
statsmodels: 0.9.0-py36h3010b51_0 defaults
tk: 8.6.8-ha92aebf_0 conda-forge
tornado: 5.1.1-py36h470a237_0 conda-forge
urllib3: 1.23-py36_1001 conda-forge
wheel: 0.32.1-py36_0 conda-forge
xerces-c: 3.2.0-h5d6a6da_2 conda-forge
xorg-kbproto: 1.0.7-h470a237_2 conda-forge
xorg-libice: 1.0.9-h470a237_4 conda-forge
xorg-libsm: 1.2.2-h8c8a85c_6 conda-forge
xorg-libx11: 1.6.6-h470a237_0 conda-forge
xorg-libxau: 1.0.8-h470a237_6 conda-forge
xorg-libxdmcp: 1.1.2-h470a237_7 conda-forge
xorg-libxext: 1.3.3-h470a237_4 conda-forge
xorg-libxrender: 0.9.10-h470a237_2 conda-forge
xorg-renderproto: 0.11.1-h470a237_2 conda-forge
xorg-xextproto: 7.3.0-h470a237_2 conda-forge
xorg-xproto: 7.0.31-h470a237_7 conda-forge
xz: 5.2.4-h470a237_1 conda-forge
yaml: 0.1.7-h470a237_1 conda-forge
zlib: 1.2.11-h470a237_3 conda-forge
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... dbus post-link :: /etc/machine-id not found ..
dbus post-link :: .. using /proc/sys/kernel/random/boot_id
done
Solving environment: ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /opt/conda/conda-bld/pygtftk_1539260246658/_build_env
The following NEW packages will be INSTALLED:
binutils_impl_linux-64: 2.31.1-h6176602_1 defaults
binutils_linux-64: 2.31.1-h6176602_3 defaults
gcc_impl_linux-64: 7.3.0-habb00fd_1 defaults
gcc_linux-64: 7.3.0-h553295d_3 defaults
libgcc-ng: 8.2.0-hdf63c60_1 defaults
libstdcxx-ng: 8.2.0-hdf63c60_1 defaults
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
INFO: activate-binutils_linux-64.sh made the following environmental changes:
+ADDR2LINE=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-addr2line
+AR=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar
+AS=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-as
+CXXFILT=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++filt
+ELFEDIT=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-elfedit
+GPROF=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-gprof
+HOST=x86_64-conda_cos6-linux-gnu
+LD_GOLD=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-ld.gold
+LD=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-ld
+NM=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-nm
+OBJCOPY=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-objcopy
+OBJDUMP=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-objdump
+RANLIB=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib
+READELF=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-readelf
+SIZE=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-size
+STRINGS=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-strings
+STRIP=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-strip
INFO: activate-gcc_linux-64.sh made the following environmental changes:
+CC=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
+CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
+CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2
+CPP=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cpp
+DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og
+GCC_AR=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
+GCC_NM=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
+GCC=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc
+GCC_RANLIB=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
+LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib
CC: /opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/version.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/bedtool_extension.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/cmd_manager.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/settings.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/biomart.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/Line.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/fasta_interface.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/cmd_object.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/tab_interface.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/utils.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/arg_formatter.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/gtf_interface.py -> build/lib.linux-x86_64-3.6/pygtftk
creating build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/nb_transcripts.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/convert.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/shift.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_nb_exon.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_numeric_value.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/bed_to_gtf.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/nb_exons.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_intron_size.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/join_multi_file.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_go.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/add_prefix.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_feat_seq.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/profile.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_loc.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/random_tx.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_5p_3p_coords.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/del_attr.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_most_5p_tx.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/count.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_tx_size.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/add_exon_nb.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/divergent.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/tss_dist.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/count_key_values.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_attr_value_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/mk_matrix.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_feature_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/intronic.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/tabulate.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_tx_seq.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/intron_size.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/closest_genes.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/short_long.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/merge_attr.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/col_from_tab.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_max_exon_nb.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/discretize_key.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/feat_size.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/join_attr.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/apropos.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/seqid_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_example.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/convergent.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/splicing_site.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_attr_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/control_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/retrieve.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/random_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/midpoints.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_key.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_regexp.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/overlapping.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/intergenic.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/exon_size.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/convert_ensembl.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/rm_dup_tss.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/coverage.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
creating build/lib.linux-x86_64-3.6/docs
copying docs/__init__.py -> build/lib.linux-x86_64-3.6/docs
Python version : sys.version_info(major=3, minor=6, micro=6, releaselevel='final', serial=0)
Python path : /opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place
Trying to find an existing .gtftk directory
No .gtftk directory found.
package init file 'docs/source/__init__.py' not found (or not a regular file)
creating build/lib.linux-x86_64-3.6/docs/source
copying docs/source/conf.py -> build/lib.linux-x86_64-3.6/docs/source
creating build/lib.linux-x86_64-3.6/pygtftk/bwig
copying pygtftk/bwig/bw_coverage.py -> build/lib.linux-x86_64-3.6/pygtftk/bwig
copying pygtftk/bwig/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/bwig
creating build/lib.linux-x86_64-3.6/pygtftk/rtools
copying pygtftk/rtools/r_plugin_parser.py -> build/lib.linux-x86_64-3.6/pygtftk/rtools
copying pygtftk/rtools/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/rtools
creating build/lib.linux-x86_64-3.6/pygtftk/data
copying pygtftk/data/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data
creating build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
creating build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
creating build/lib.linux-x86_64-3.6/pygtftk/data/simple_03
copying pygtftk/data/simple_03/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_03
creating build/lib.linux-x86_64-3.6/pygtftk/data/simple_04
copying pygtftk/data/simple_04/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_04
creating build/lib.linux-x86_64-3.6/pygtftk/data/simple_05
copying pygtftk/data/simple_05/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_05
creating build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
creating build/lib.linux-x86_64-3.6/pygtftk/data/mini_real_noov_rnd_tx
copying pygtftk/data/mini_real_noov_rnd_tx/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real_noov_rnd_tx
creating build/lib.linux-x86_64-3.6/pygtftk/data/control_list
copying pygtftk/data/control_list/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/control_list
creating build/lib.linux-x86_64-3.6/pygtftk/src
copying pygtftk/src/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/src
creating build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
creating build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying docs/Makefile -> build/lib.linux-x86_64-3.6/docs
copying docs/source/bwig_coverage.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/about.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/api.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/installation.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/developers.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/index.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/presentation.rst -> build/lib.linux-x86_64-3.6/docs/source
copying pygtftk/data/simple/simple_col.csv -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.join -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.join_mat -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.genes -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple_peaks.bed3 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.join_with_dup -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.2.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.1.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.map -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.3.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple_peaks.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple_peaks.bed6 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.fa.fai -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.bam.bai -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.chromInfo -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.join_mat_3 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.rev.1.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.3.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple_reads.fq -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.geneList -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/add_attr_to_pos.tab -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.rev.2.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.bam -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.loc_bed -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.join_mat_2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.2.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.4.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.fa -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple_02/simple_02.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.join_mat -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.map -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.rev.1.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02_nbe.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.bam.bai -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.genes -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.2.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02_nbe.gtf.old -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.reads.fq -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.rev.2.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.join -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.geneList -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.chromInfo -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02_peaks.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.fa -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.3.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.1.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.4.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.bam -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_03/simple_short_long.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_03
copying pygtftk/data/simple_04/simple.chromInfo -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_04
copying pygtftk/data/simple_04/simple_04.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_04
copying pygtftk/data/simple_04/simple_04.fa -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_04
copying pygtftk/data/simple_05/simple_rm.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_05
copying pygtftk/data/mini_real/H3K4me3_cond_1.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/mini_real_control_1.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/#H3K4me3_cond_1.bed# -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/mini_real_counts_ENCFF630HEX.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF431HAA_H3K36me3_K562_sub.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/airway_love.txt.gz -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/mini_real.gtf.gz -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF119BYM_H3K36me3_K562_sub.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/tx_classes.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF742FDS_H3K4me3_K562_sub.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/mini_real_gn_list_hg38.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/hg38.genome.back -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF947DVY_H3K79me2_K562_sub.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/hg38.genome -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/H3K4me3_cond_3.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF112BHN_H3K4me3_K562_sub.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF354QXX__H3K79me2_K562_sub.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/H3K4me3_cond_2.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real_noov_rnd_tx/mini_real_noov_rnd_tx.gtf.gz -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real_noov_rnd_tx
copying pygtftk/data/mini_real_noov_rnd_tx/hg38.genome -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real_noov_rnd_tx
copying pygtftk/data/control_list/control_list_reference.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/control_list
copying pygtftk/data/control_list/control_list_data.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/control_list
copying pygtftk/src/libgtftk/column.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/README.md -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/gtf_reader.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/globals.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/libgtftk.h -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/version.h -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/libgtftk.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/blast_reader.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/command/select_by_genomic_location.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/merge_attr.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/load_blast.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/load_gtf.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/free_raw_data.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/free_gtf_data.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/add_attributes.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/select_by_key.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/get_sequences.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/clear_indexes.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/select_by_transcript_size.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/convert_to_ensembl.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/add_prefix.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/select_by_number_of_exon.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/add_exon_number.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/select_by_positions.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/del_attributes.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/select_transcript.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/extract_data.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/get_list.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/add_attr_column.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/add_attr_to_pos.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
running build_ext
building 'pygtftk/lib/libgtftk' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/pygtftk
creating build/temp.linux-x86_64-3.6/pygtftk/src
creating build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk
creating build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/blast_reader.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/blast_reader.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/add_attributes.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attributes.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/add_attr_to_pos.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_to_pos.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/load_blast.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_blast.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/merge_attr.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/merge_attr.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_by_positions.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_positions.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/add_attr_column.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_column.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_transcript.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_transcript.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/add_exon_number.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_exon_number.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/add_prefix.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_prefix.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/libgtftk.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/libgtftk.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/free_raw_data.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_raw_data.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/column.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/column.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/free_gtf_data.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_gtf_data.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_by_number_of_exon.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_number_of_exon.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/convert_to_ensembl.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/convert_to_ensembl.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/extract_data.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/extract_data.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_by_genomic_location.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_genomic_location.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/clear_indexes.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/clear_indexes.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/get_list.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_list.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_by_key.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_key.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/get_sequences.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_sequences.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/globals.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/globals.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/del_attributes.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/del_attributes.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/load_gtf.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_gtf.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/gtf_reader.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/gtf_reader.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_by_transcript_size.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_transcript_size.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
creating build/lib.linux-x86_64-3.6/pygtftk/lib
gcc -pthread -shared -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -Wl,-rpath=/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib,--no-as-needed -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -Wl,-rpath=/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib,--no-as-needed -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/blast_reader.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attributes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_to_pos.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_blast.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/merge_attr.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_positions.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_column.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_transcript.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_exon_number.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_prefix.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/libgtftk.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_raw_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/column.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_gtf_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_number_of_exon.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/convert_to_ensembl.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/extract_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_genomic_location.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/clear_indexes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_list.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_key.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_sequences.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/globals.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/del_attributes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_gtf.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/gtf_reader.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_transcript_size.o -L/usr/lib -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -lz -lpython3.6m -o build/lib.linux-x86_64-3.6/pygtftk/lib/libgtftk.cpython-36m-x86_64-linux-gnu.so
error: command 'gcc' failed with exit status 1
Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: 0.9.7_6ce8e5d235.tar.gz
Downloading https://github.com/dputhier/pygtftk/archive/0.9.7.tar.gz
Success
Extracting download
source tree in: /opt/conda/conda-bld/pygtftk_1539260246658/work
Traceback (most recent call last):
File "/opt/conda/bin/conda-build", line 11, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 438, in main
execute(sys.argv[1:])
File "/opt/conda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 429, in execute
verify=args.verify)
File "/opt/conda/lib/python3.6/site-packages/conda_build/api.py", line 201, in build
notest=notest, need_source_download=need_source_download, variants=variants)
File "/opt/conda/lib/python3.6/site-packages/conda_build/build.py", line 2204, in build_tree
notest=notest,
File "/opt/conda/lib/python3.6/site-packages/conda_build/build.py", line 1445, in build
utils.check_call_env(cmd, env=env, cwd=src_dir, stats=build_stats)
File "/opt/conda/lib/python3.6/site-packages/conda_build/utils.py", line 313, in check_call_env
return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
File "/opt/conda/lib/python3.6/site-packages/conda_build/utils.py", line 293, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/opt/conda/conda-bld/pygtftk_1539260246658/work/conda_build.sh']' returned non-zero exit status 1.
Setup.py could contain an extra_require slot in setup()
As an example:
setup(
name="my_package",
# (...)
install_requires=[
'requests',
'simplejson'],
extras_require={
'tests': [
'nose',
'pycodestyle >= 2.1.0'],
'docs': [
'sphinx >= 1.4',
'sphinx_rtd_theme']}
)
gtftk retrieve -c and -o should be mutually exclusive
Todo.
Example file
Ensure all tests are not related to any directory.
select_by_key should throw an error when no key/val is available.
Example:
gtftk join_attr -i simple.gtf -j simple.join_mat -k gene_id -V 2 -m -t exon | gtftk select_by_key
Conda dist of pygtftk not available under OSX
One of the main developpers is working under OSX :).
Select most common tss among transcript
I was wondering about a command allowing the selection of the most commonly used TSSs among transcripts described for a gene.
check self.__dict__ upon deletion of an attribute
Upon gtf.del_attr(...) the corresponding key should be deleted from self.dict and GTF._instance_attr.
To be checked.
gtftk main program complains when an unknow argument is passed
gtftk -j
AttributeError: 'ArgumentParser' object has no attribute 'allow_abbrev'
issue with select_by_regexp
The command uses re.match. It should use re.search. Will be fixed in the next release.
compatible python3
The pygtftk library should be compatible with Py3k.
peak_anno: "frequencies has a zero element at %s." % (zeropos,)) ValueError: The internally computed table of expected frequencies has a zero element at (13, 0).
Hi,
When running peak_anno with example files (containing only features on chr1) and full chromosome table/size, peak_anno crash:
gtftk peak_anno -i pygtftk/data/mini_real/mini_real.gtf.gz -o toto -c pygtftk/data/mini_real/hg38.genome -p pygtftk/data/mini_real/ENCFF112BHN_H3K4me3_K562_sub.bed -V 3
|-- 11:27:24-INFO-peak_anno : Checking chromosome info file.
|-- 11:27:24-INFO-peak_anno : Instantiating a GTF.
|-- 11:27:25-DEBUG-peak_anno : Calling extract_data_iter.
|-- 11:27:25-DEBUG-peak_anno : Ensembl format detected.
|-- 11:27:25-DEBUG_MEM-peak_anno : GTF created (#l=137670, p=0x7fc53fbd1110, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808999288, n=1).
|-- 11:27:25-DEBUG-peak_anno : Calling select_by_key (key=seqid, value=chr1,chr2,chr3,chr4...)
|-- 11:27:25-INFO-peak_anno : Found file pygtftk/data/mini_real/mini_real.gtf.gz
|-- 11:27:25-INFO-peak_anno : Instantiating a GTF.
|-- 11:27:25-DEBUG_MEM-peak_anno : GTF created (#l=137670, p=0x7fc54737f530, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808971736, n=2).
|-- 11:27:25-DEBUG_MEM-peak_anno : GTF deleted (#l=137670, p=0x7fc53fbd1110, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808999288, n=1).
|-- 11:27:25-DEBUG-peak_anno : Calling 'get_chroms'.
|-- 11:27:25-DEBUG-peak_anno : Calling 'get_feature_list'.
|-- 11:27:25-DEBUG-peak_anno : Calling extract_data (feature).
|-- 11:27:26-DEBUG-peak_anno : Calling select_by_key (key=feature, value=gene)
|-- 11:27:26-INFO-peak_anno : Found file pygtftk/data/mini_real/mini_real.gtf.gz
|-- 11:27:26-INFO-peak_anno : Instantiating a GTF.
|-- 11:27:26-DEBUG_MEM-peak_anno : GTF created (#l=1058, p=0x7fc52d9cac80, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808693152, n=3).
|-- 11:27:26-DEBUG-peak_anno : Calling 'to_bed' method.
|-- 11:27:26-DEBUG-peak_anno : Calling extract_data (seqid,start,end,score,strand,transcript_id,gene_id,exon_id).
|-- 11:27:26-DEBUG_MEM-peak_anno : GTF deleted (#l=1058, p=0x7fc52d9cac80, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808693152, n=3).
|-- 11:27:26-INFO-peak_anno : Beginning shuffling for a given set of features...
|-- 11:27:26-DEBUG-peak_anno : BATCHES : 10 batches of 20 shuffles
|-- 11:27:26-DEBUG-peak_anno : Total number of shuffles : 200
|-- 11:27:26-DEBUG-peak_anno : NB_THREADS = 8
|-- 11:27:26-DEBUG-peak_anno : BED files read as lists of intervals in 0.17975282669067383 s
|-- 11:27:26-INFO-peak_anno : --- Minibatch nb. : 1 / 10
|-- 11:27:26-DEBUG-peak_anno : Batch generated and shuffled in 0.023317813873291016 s
|-- 11:27:26-DEBUG-peak_anno : Batch converted to fake beds in : 0.1311180591583252 s
|-- 11:27:27-DEBUG-peak_anno : All intersections computed by custom code in : 0.6467368602752686 s
|-- 11:27:27-INFO-peak_anno : --- Minibatch nb. : 2 / 10
|-- 11:27:27-DEBUG-peak_anno : Batch generated and shuffled in 0.019360065460205078 s
|-- 11:27:27-DEBUG-peak_anno : Batch converted to fake beds in : 0.12729096412658691 s
|-- 11:27:28-DEBUG-peak_anno : All intersections computed by custom code in : 0.6355540752410889 s
|-- 11:27:28-INFO-peak_anno : --- Minibatch nb. : 3 / 10
|-- 11:27:28-DEBUG-peak_anno : Batch generated and shuffled in 0.018916845321655273 s
|-- 11:27:28-DEBUG-peak_anno : Batch converted to fake beds in : 0.13068914413452148 s
|-- 11:27:28-DEBUG-peak_anno : All intersections computed by custom code in : 0.6408717632293701 s
|-- 11:27:28-INFO-peak_anno : --- Minibatch nb. : 4 / 10
|-- 11:27:28-DEBUG-peak_anno : Batch generated and shuffled in 0.0192258358001709 s
|-- 11:27:29-DEBUG-peak_anno : Batch converted to fake beds in : 0.12983202934265137 s
|-- 11:27:29-DEBUG-peak_anno : All intersections computed by custom code in : 0.6501920223236084 s
|-- 11:27:29-INFO-peak_anno : --- Minibatch nb. : 5 / 10
|-- 11:27:29-DEBUG-peak_anno : Batch generated and shuffled in 0.0198819637298584 s
|-- 11:27:29-DEBUG-peak_anno : Batch converted to fake beds in : 0.13089895248413086 s
|-- 11:27:30-DEBUG-peak_anno : All intersections computed by custom code in : 0.7375490665435791 s
|-- 11:27:30-INFO-peak_anno : --- Minibatch nb. : 6 / 10
|-- 11:27:30-DEBUG-peak_anno : Batch generated and shuffled in 0.020968914031982422 s
|-- 11:27:30-DEBUG-peak_anno : Batch converted to fake beds in : 0.1310739517211914 s
|-- 11:27:31-DEBUG-peak_anno : All intersections computed by custom code in : 0.7431747913360596 s
|-- 11:27:31-INFO-peak_anno : --- Minibatch nb. : 7 / 10
|-- 11:27:31-DEBUG-peak_anno : Batch generated and shuffled in 0.01874995231628418 s
|-- 11:27:31-DEBUG-peak_anno : Batch converted to fake beds in : 0.1322779655456543 s
|-- 11:27:32-DEBUG-peak_anno : All intersections computed by custom code in : 0.6475603580474854 s
|-- 11:27:32-INFO-peak_anno : --- Minibatch nb. : 8 / 10
|-- 11:27:32-DEBUG-peak_anno : Batch generated and shuffled in 0.0187680721282959 s
|-- 11:27:32-DEBUG-peak_anno : Batch converted to fake beds in : 0.12628579139709473 s
|-- 11:27:33-DEBUG-peak_anno : All intersections computed by custom code in : 0.7448949813842773 s
|-- 11:27:33-INFO-peak_anno : --- Minibatch nb. : 9 / 10
|-- 11:27:33-DEBUG-peak_anno : Batch generated and shuffled in 0.019285917282104492 s
|-- 11:27:33-DEBUG-peak_anno : Batch converted to fake beds in : 0.13170504570007324 s
|-- 11:27:34-DEBUG-peak_anno : All intersections computed by custom code in : 0.7476060390472412 s
|-- 11:27:34-INFO-peak_anno : --- Minibatch nb. : 10 / 10
|-- 11:27:34-DEBUG-peak_anno : Batch generated and shuffled in 0.018893003463745117 s
|-- 11:27:34-DEBUG-peak_anno : Batch converted to fake beds in : 0.12927627563476562 s
|-- 11:27:35-DEBUG-peak_anno : All intersections computed by custom code in : 0.7500202655792236 s
|-- 11:27:35-DEBUG-peak_anno : All intersections have been generated.
|-- 11:27:35-DEBUG-peak_anno : Statistics on overlaps computed in : 0.12702703475952148 s
Traceback (most recent call last):
File "/Users/puthier/miniconda3/envs/pygtftk/bin/gtftk", line 4, in <module>
__import__('pkg_resources').run_script('pygtftk==0.9.9.dev0+cbb3', 'gtftk')
File "/Users/puthier/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 661, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/Users/puthier/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1441, in run_script
exec(code, namespace, namespace)
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/EGG-INFO/scripts/gtftk", line 104, in <module>
args = main()
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/EGG-INFO/scripts/gtftk", line 89, in main
CmdManager.run(args)
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/cmd_manager.py", line 950, in run
fun(**args)
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/plugins/peak_anno.py", line 457, in peak_anno
hits[feat_type] = overlap_partial(bedA=peak_file, bedB=gtf_sub_bed)
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/overlap_stats_shuffling.py", line 229, in compute_overlap_stats
ps = nf.check_negbin_adjustment(summed_bp_overlaps, esperance_fitted_summed_bp_overlaps, variance_fitted_summed_bp_overlaps)#.pvalue
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/negbin_fit.py", line 90, in check_negbin_adjustment
result = 1 - cramers_V(crosstab)
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/negbin_fit.py", line 84, in cramers_V
chi2 = scipy.stats.chi2_contingency(crosstab)[0]
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/scipy/stats/contingency.py", line 253, in chi2_contingency
"frequencies has a zero element at %s." % (zeropos,))
ValueError: The internally computed table of expected frequencies has a zero element at (13, 0).
|-- 11:27:44-DEBUG_MEM-peak_anno : GTF deleted (#l=0, p=0x7fc54737f530, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808971736, n=2).
puthier (pygtftk)
peak_anno_shuffling ● ? ⍟5 …/pygtftk gtftk peak_anno -i pygtftk/data/mini_real/mini_real.gtf.gz -o toto -c pygtftk/data/mini_real/hg38.genome -p pygtftk/data/mini_real/ENCFF112BHN_H3K4me3_K562_sub.bed -V 3
$RPROMPT_PREFIX$(build_right_prompt)$reset_color$RPROMPT_SUFFIX
puthier (pygtftk)
peak_anno_shuffling ● ? ⍟5 …/pygtftk gunzip -c pygtftk/data/mini_real/mini_real.gtf.gz| less 1 ↵ ⚙ 10067 11:28:07
puthier (pygtftk)
peak_anno_shuffling ● ? ⍟5 …/pygtftk less pygtftk/data/mini_real/hg38.genome PIPE(-13)|0 ↵ ⚙ 10068 11:28:16
puthier (pygtftk)
peak_anno_shuffling ● ? ⍟5 …/pygtftk cp pygtftk/data/mini_real/hg38.genome hg38 ✔ ⚙ 10069 11:28:26
puthier (pygtftk)
peak_anno_shuffling ● ? ⍟5 …/pygtftk gtftk peak_anno -i pygtftk/data/mini_real/mini_real.gtf.gz -o toto -c hg38 -p pygtftk/data/mini_real/ENCFF112BHN_H3K4me3_K562_sub.bed -V 3
|-- 11:28:53-INFO-peak_anno : Checking chromosome info file.
|-- 11:28:53-INFO-peak_anno : Instantiating a GTF.
|-- 11:28:53-DEBUG-peak_anno : Calling extract_data_iter.
|-- 11:28:53-DEBUG-peak_anno : Ensembl format detected.
|-- 11:28:53-DEBUG_MEM-peak_anno : GTF created (#l=137670, p=0x7fb5380d4010, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120752028752, n=1).
|-- 11:28:53-DEBUG-peak_anno : Calling select_by_key (key=seqid, value=chr1,chr2,chr3,chr4...)
|-- 11:28:54-INFO-peak_anno : Found file pygtftk/data/mini_real/mini_real.gtf.gz
|-- 11:28:54-INFO-peak_anno : Instantiating a GTF.
|-- 11:28:54-DEBUG_MEM-peak_anno : GTF created (#l=137670, p=0x7fb5380e3840, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120752000528, n=2).
|-- 11:28:54-DEBUG_MEM-peak_anno : GTF deleted (#l=137670, p=0x7fb5380d4010, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120752028752, n=1).
|-- 11:28:54-DEBUG-peak_anno : Calling 'get_chroms'.
|-- 11:28:54-DEBUG-peak_anno : Calling 'get_feature_list'.
|-- 11:28:54-DEBUG-peak_anno : Calling extract_data (feature).
|-- 11:28:55-DEBUG-peak_anno : Calling select_by_key (key=feature, value=gene)
|-- 11:28:55-INFO-peak_anno : Found file pygtftk/data/mini_real/mini_real.gtf.gz
|-- 11:28:55-INFO-peak_anno : Instantiating a GTF.
|-- 11:28:55-DEBUG_MEM-peak_anno : GTF created (#l=1058, p=0x7fb5380d7eb0, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120751718296, n=3).
|-- 11:28:55-DEBUG-peak_anno : Calling 'to_bed' method.
|-- 11:28:55-DEBUG-peak_anno : Calling extract_data (seqid,start,end,score,strand,transcript_id,gene_id,exon_id).
|-- 11:28:55-DEBUG_MEM-peak_anno : GTF deleted (#l=0, p=0x7fb5380d7eb0, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120751718296, n=3).
|-- 11:28:55-INFO-peak_anno : Beginning shuffling for a given set of features...
|-- 11:28:55-DEBUG-peak_anno : BATCHES : 10 batches of 20 shuffles
|-- 11:28:55-DEBUG-peak_anno : Total number of shuffles : 200
|-- 11:28:55-DEBUG-peak_anno : NB_THREADS = 8
|-- 11:28:55-DEBUG-peak_anno : BED files read as lists of intervals in 0.15019702911376953 s
|-- 11:28:55-INFO-peak_anno : --- Minibatch nb. : 1 / 10
|-- 11:28:55-DEBUG-peak_anno : Batch generated and shuffled in 0.018970966339111328 s
|-- 11:28:55-DEBUG-peak_anno : Batch converted to fake beds in : 0.13421201705932617 s
|-- 11:28:56-DEBUG-peak_anno : All intersections computed by custom code in : 0.6478052139282227 s
|-- 11:28:56-INFO-peak_anno : --- Minibatch nb. : 2 / 10
|-- 11:28:56-DEBUG-peak_anno : Batch generated and shuffled in 0.01854705810546875 s
|-- 11:28:56-DEBUG-peak_anno : Batch converted to fake beds in : 0.1281449794769287 s
|-- 11:28:56-DEBUG-peak_anno : All intersections computed by custom code in : 0.6428921222686768 s
|-- 11:28:56-INFO-peak_anno : --- Minibatch nb. : 3 / 10
|-- 11:28:56-DEBUG-peak_anno : Batch generated and shuffled in 0.01955699920654297 s
|-- 11:28:57-DEBUG-peak_anno : Batch converted to fake beds in : 0.13239288330078125 s
|-- 11:28:57-DEBUG-peak_anno : All intersections computed by custom code in : 0.6378078460693359 s
|-- 11:28:57-INFO-peak_anno : --- Minibatch nb. : 4 / 10
|-- 11:28:57-DEBUG-peak_anno : Batch generated and shuffled in 0.01935100555419922 s
|-- 11:28:57-DEBUG-peak_anno : Batch converted to fake beds in : 0.1293799877166748 s
|-- 11:28:58-DEBUG-peak_anno : All intersections computed by custom code in : 0.6441848278045654 s
|-- 11:28:58-INFO-peak_anno : --- Minibatch nb. : 5 / 10
|-- 11:28:58-DEBUG-peak_anno : Batch generated and shuffled in 0.018750905990600586 s
|-- 11:28:58-DEBUG-peak_anno : Batch converted to fake beds in : 0.1291358470916748 s
|-- 11:28:59-DEBUG-peak_anno : All intersections computed by custom code in : 0.6483819484710693 s
|-- 11:28:59-INFO-peak_anno : --- Minibatch nb. : 6 / 10
|-- 11:28:59-DEBUG-peak_anno : Batch generated and shuffled in 0.019301176071166992 s
|-- 11:28:59-DEBUG-peak_anno : Batch converted to fake beds in : 0.13379311561584473 s
|-- 11:29:00-DEBUG-peak_anno : All intersections computed by custom code in : 0.6421530246734619 s
|-- 11:29:00-INFO-peak_anno : --- Minibatch nb. : 7 / 10
|-- 11:29:00-DEBUG-peak_anno : Batch generated and shuffled in 0.018435001373291016 s
|-- 11:29:00-DEBUG-peak_anno : Batch converted to fake beds in : 0.1339731216430664 s
|-- 11:29:00-DEBUG-peak_anno : All intersections computed by custom code in : 0.7524068355560303 s
|-- 11:29:00-INFO-peak_anno : --- Minibatch nb. : 8 / 10
|-- 11:29:01-DEBUG-peak_anno : Batch generated and shuffled in 0.018976926803588867 s
|-- 11:29:01-DEBUG-peak_anno : Batch converted to fake beds in : 0.13104987144470215 s
|-- 11:29:01-DEBUG-peak_anno : All intersections computed by custom code in : 0.7570860385894775 s
|-- 11:29:01-INFO-peak_anno : --- Minibatch nb. : 9 / 10
|-- 11:29:01-DEBUG-peak_anno : Batch generated and shuffled in 0.01871800422668457 s
|-- 11:29:02-DEBUG-peak_anno : Batch converted to fake beds in : 0.1300792694091797 s
|-- 11:29:02-DEBUG-peak_anno : All intersections computed by custom code in : 0.7510981559753418 s
|-- 11:29:02-INFO-peak_anno : --- Minibatch nb. : 10 / 10
|-- 11:29:02-DEBUG-peak_anno : Batch generated and shuffled in 0.018780946731567383 s
|-- 11:29:02-DEBUG-peak_anno : Batch converted to fake beds in : 0.1317291259765625 s
|-- 11:29:03-DEBUG-peak_anno : All intersections computed by custom code in : 0.7473132610321045 s
|-- 11:29:03-DEBUG-peak_anno : All intersections have been generated.
|-- 11:29:03-DEBUG-peak_anno : Statistics on overlaps computed in : 0.1287541389465332 s
Traceback (most recent call last):
File "/Users/puthier/miniconda3/envs/pygtftk/bin/gtftk", line 4, in <module>
__import__('pkg_resources').run_script('pygtftk==0.9.9.dev0+cbb3', 'gtftk')
File "/Users/puthier/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 661, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/Users/puthier/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1441, in run_script
exec(code, namespace, namespace)
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/EGG-INFO/scripts/gtftk", line 104, in <module>
args = main()
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/EGG-INFO/scripts/gtftk", line 89, in main
CmdManager.run(args)
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/cmd_manager.py", line 950, in run
fun(**args)
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/plugins/peak_anno.py", line 457, in peak_anno
hits[feat_type] = overlap_partial(bedA=peak_file, bedB=gtf_sub_bed)
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/overlap_stats_shuffling.py", line 229, in compute_overlap_stats
ps = nf.check_negbin_adjustment(summed_bp_overlaps, esperance_fitted_summed_bp_overlaps, variance_fitted_summed_bp_overlaps)#.pvalue
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/negbin_fit.py", line 90, in check_negbin_adjustment
result = 1 - cramers_V(crosstab)
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/negbin_fit.py", line 84, in cramers_V
chi2 = scipy.stats.chi2_contingency(crosstab)[0]
File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/scipy/stats/contingency.py", line 253, in chi2_contingency
"frequencies has a zero element at %s." % (zeropos,))
ValueError: The internally computed table of expected frequencies has a zero element at (13, 0).
|-- 11:29:13-DEBUG_MEM-peak_anno : GTF deleted (#l=137670, p=0x7fb5380e3840, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120752000528, n=2).
Blast output to GTF
It could be interesting to propose a blast to gff/gtf output as required in this post on biostar:
https://www.biostars.org/p/277/
Some temporary files are left
The worker_coverage_* files are not added to pygtftk.utils.TMP_FILE_LIST. Most likely due to some concurrency issues when using pool.
peak_anno: idea for new argument "-rpm"
This argument would normalize reads count to RPM (Reads in feature per million reads in sample). This would allow easier comparison of plots produced for different samples. The plot would also contains the normalization factor.
Thx Guillaume.
Peak_anno new feature idea: --peak-file taking list instead of only one file
It would imply giving fraction of overlaps instead of number of overlaps which depend on the number of peaks. This would not require so much modifications.
- change the argument type to action=a arg_formatter.bedFileList .
- Add a novel argument to set order of peak dataset inside bar sets.
- Some tuning regarding the R code mainly when writing p-val results.
Thx Guillaume for this idea.
Exit code 247 on readthedoc
I had recurrent issues with building on readthedoc with an exit code 247. I managed to fix it in commit 6e8439c by deleting some conda channels. This could maybe help others in the future...
get_tx_seq: should accept genome in gz format without complaining.
Morever the GlobbedFileList action does not throw error when file does not exist nor complain if the extension is the wrong one.
hide_undef is not supported by extract_data when a TAB object is returned
import pygtftk.utils
from pygtftk.utils import get_example_file
from tempfile import NamedTemporaryFile
from pygtftk.gtf_interface import GTF
a_file = get_example_file()[0]
gtf = GTF("Homo_sapiens.GRCh38.91.chr.gtf.gz")
a = gtf.extract_data("start,end,transcript_id", hide_undef=True)
Distutils package at installation - 'ftputils'
During installation with the pip install pygtftk command, an error occurs when trying to uninstall ftputils 3.2, presumably to install a pygtftk-compatible version :
"Cannot uninstall 'ftputil'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall."
Workaround : calling the installation with pip install --ignore-installed pygtftk results in pip skipping the package and installing correctly pygtftk, but this is not a viable solution as it will lead to older packages being kept and could result in a dependency error.
Get the closest gene regarding a set of peaks.
Loosen dep requirements
argformatter: bed6 and FileWithExtension should be merge
Both should be merged into a single class/action
file_format(mode='r', file_ext='bed')
retrieve usage in interpreter
When using retrieve inside an interpreter, setting the output file name to the expected one (i.e. name of the downloaded file from ftp) result in no download. This may be due to 'ftp.download_if_newer()' on line 264 of retrieve.py.
import pygtftk.utils
from pygtftk.utils import get_example_file
from tempfile import NamedTemporaryFile
from pygtftk.gtf_interface import GTF
from pygtftk.plugins.retrieve import retrieve
retrieve(species_name='homo_sapiens', release='91', outputfile=open('Homo_sapiens.GRCh38.91.chr.gtf.gz', 'w')
...: )
closest_gn_to_feat output format
Should be centered on gene or peaks.
Should provided some flexibility about gene features (tts, tss, body).
Is a peak or gene associated with several guys ?
Code improvement
In line 312 in Line.py, a While loop should be used instead of the ugly:
for k, v in zip(ptr.attributes.attr[0:self.nb_key], ptr.attributes.attr[0:self.nb_key]):
self.attr[ffi.string(k.key).decode()] = ffi.string(v.value).decode()
get_tx_seq sequence truncated.
In version 0.9.8 get_tx_seq do not return properly the sequence. It seems that most sequences on minus strand are truncated. This was not highlighted by tests that, in this case, use short artificial transcripts. This should be fixed and new tests added.
argparse should not be a dependency
It is part of Python 3. This would install an old version...
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