Easy to use. Plug into other tools. Platform independence.

I think poretools began the "trend" of embedding the path to the fast5 file in the FASTA/Q header. I want to formalise and standardise this so we can embed more information in the header, and I suggest something along the lines of UniProt which embedds tag=value in the header:

http://www.uniprot.org/help/fasta-headers

db|UniqueIdentifier|EntryName ProteinName OS=OrganismName GN=GeneName PE=ProteinExistence SV=SequenceVersion

(obviously we'd need to design our own tags)

I can't really think of any strong objections to this, but would be happy to listen?

Before we discuss FASTQ, I'd need to understand why ":" was chosen for the separator and not whitespace?

If we can agree on this, we need to discuss with others e.g. NanoOK, minoTour, MetaPore

Cheers
Mick

If we used ggvis we could produce web-browser ready reports which would also fix the Windows interactive viewer problem (http://ggvis.rstudio.com/).

Can I suggest that you give (as an option) an output directory for squiggles? It currently outputs(I think) in the same dir as the fast5, not always ideal.

New Metrichor makes a directory 'filtered' and a directory 'the_rest' for basic QC filtering. Therefore it might be nice to offer a recursive (-r ?) option to all poretools utilities that work on Fast5 sets in order to analyse both directories at once.

Hi all,

In the last version of Metrichor I think that the 1D data have been moved from /Analyses/Basecall_2D_000/ to /Analyses/Basecall_1D_000/
Have you also noticed this ?

Have a nice day.
Stefan Engelen

It would be convenient to create a single HDF5 file of all the FAST5 files from a run. This would prevent superfluous I/O (e.g., open() for every read/file) and make runs more managable/portable.

At the moment you can only specify one directory, or it assumes they are all files. Not sure how to implement this efficiently?

the --saveas option does not work with poretools squiggle.

$ poretools squiggle --saveas test.png my.fast5
usage: poretools squiggle [-h] [-q] [--saveas STRING] [--num-facets INTEGER]
                          [--theme-bw]
                          FILES [FILES ...]
poretools squiggle: error: argument --saveas: invalid choice: 'test.png' (choose from 'pdf', 'png')

In tabular form.

I was getting consistent install failures on my Mac using sudo python setup.py install, with the following error always coming up:

Processing dependencies for poretools==0.5.1
Searching for h5py>=2.0.0
Reading http://pypi.python.org/simple/h5py/
Reading http://code.google.com/p/h5py/downloads/list
Reading http://h5py.alfven.org
Reading http://www.h5py.org
Best match: h5py 2.4.0
Downloading https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz#md5=80c9a94ae31f84885cc2ebe1323d6758
Processing h5py-2.4.0.tar.gz
Running h5py-2.4.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-ljfYlb/h5py-2.4.0/egg-dist-tmp-aWgyQ0
warning: no previously-included files found matching 'h5py/defs.pyx'
warning: no previously-included files found matching 'h5py/defs.pxd'
warning: no previously-included files found matching 'h5py/config.pxi'
Autodetected HDF5 1.8.14
********************************************************************************
                       Summary of the h5py configuration

    Path to HDF5: None
    HDF5 Version: '1.8.14'
    MPI Enabled: False
    Rebuild Required: False

********************************************************************************
Executing api\_gen rebuild of refs
clang: error: no such file or directory: '/tmp/easy_install-ljfYlb/h5py-2.4.0/h5py/defs.c'

That appears to be due to a failure to install/compile h5py, but I already have that include in my python site packages. To get around the error I deleted the h5py requirement from the requirements.txt and the install then went correctly. I haven't had any issues using poretools by doing that, so I figured I would let you know in case any other users encounter a similar issue.

Cheers,
Mike

Hi, all
I got the output of with the command "poretools events /path/to/data ". However the meaning of every column really confuses me. I also searched the Internet and found nothing.
Could someone help me?
Thanks very much.

Should be a straight forward change to the path in the FAST5 file.

Should probably be used for poretools fasta/fastq functions.

This was omitted because of an oversight.

Again, I think poretools began the trend of adding "_twodirections" to the read ID (for 2D reads). I'm not sure I like it.

There are no standards, but I guess what comes from the Illumina world is that relationships between reads are embedded in the filenames containing those reads, and the order within those files (_R1.fastq and _R2.fastq). It's not perfect, but it avoids altering the read IDs (and we should always avoid altering primary data), and means we don't need to do string manipulation on read IDs before comparing them (or do partial string matching).

If we absolutely, 100% think we need to change the read identifiers, can I suggest:

.2d
.t
.c

which is a lot simpler? (this is quite similar to the /1 and /2 from old Illumina/Solexa identifiers, which were done away with, presumably for a reason)

Cheers
Mick

Nicks-Mac:~ nick$ sudo pip install poretools --upgrade
Downloading/unpacking poretools from https://pypi.python.org/packages/source/p/poretools/poretools-0.5.0.tar.gz#md5=4ea39e676895198ba086bb97a0617406
Downloading poretools-0.5.0.tar.gz
Running setup.py (path:/private/tmp/pip_build_root/poretools/setup.py) egg_info for package poretools
Traceback (most recent call last):
File "", line 17, in
File "/private/tmp/pip_build_root/poretools/setup.py", line 11, in
with open("requirements.txt", "r") as f:
IOError: [Errno 2] No such file or directory: 'requirements.txt'
Complete output from command python setup.py egg_info:
Traceback (most recent call last):

File "", line 17, in

File "/private/tmp/pip_build_root/poretools/setup.py", line 11, in

with open("requirements.txt", "r") as f:

IOError: [Errno 2] No such file or directory: 'requirements.txt'

Cleaning up...
Command python setup.py egg_info failed with error code 1 in /private/tmp/pip_build_root/poretools
Storing debug log for failure in /Users/nick/Library/Logs/pip.log

Error: reading '/dev/shm/pore-load.ghitty.tmp/LomanLabz_E.coli_MG1655_3311_1_ch495_file5_strand.fast5'
Traceback (most recent call last):
  File "pore-load.py", line 176, in ReadFast5Data
    rslt.readno = f5.get_read_number()
  File "/home/durbrowk/.local/lib/python2.7/site-packages/poretools-0.5.1-py2.7.egg/poretools/Fast5File.py", line 363, in get_read_number
    node = self.find_read_number_block()
  File "/home/durbrowk/.local/lib/python2.7/site-packages/poretools-0.5.1-py2.7.egg/poretools/Fast5File.py", line 343, in find_read_number_block
    newpath = "/" + "/".join(path.path.split("/")[:-1])
AttributeError: 'NoneType' object has no attribute 'path'

I don't mind the error, but perhaps it would be cleaner to catch it inside of poretools and return None for the read number.

It would be nice if there was a documented way to determine if a .fast5 file contains any usable data at all. I currently first use h5py to see if the .fast5 file is actually HDF5 at all (sometimes it's HTML containing an error message), and then I try to pull the data from it using poretools inside of a try block and assume that any error I get is because the file was bad.

By the way, h5dump can't read that file either.

h5dump /dev/shm/pore-load.ghitty.tmp/LomanLabz_E.coli_MG1655_3311_1_ch495_file5_strand.fast5
h5dump error: internal error (file /home/hdftest/snapshots-bin-hdf5_1_8_10/current/tools/h5dump/h5dump.c:line 1539)
HDF5: infinite loop closing library
      D,G,T,F,FD,P,FD,P,FD,P,E,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL

Hello,

I got this error when running poretools twice simultaneously:

OSError: [Errno 39] Directory not empty: '.poretools_tmp/H566_ON_inc'

It would be useful to fix this, and I guess it could be done by using tempfile.mkdtemp, instead of the static name '.poretools_tmp'.

I hope that helps.
Have a nice day,
Martin Frith

P.S. Full error message:

Traceback (most recent call last):
File "/usr/local/bin/poretools", line 9, in
load_entry_point('poretools==0.5.1', 'console_scripts', 'poretools')()
File "/usr/local/lib/python2.7/dist-packages/poretools-0.5.1-py2.7.egg/poretools/poretools_main.py", line 401, in main
args.func(parser, args)
File "/usr/local/lib/python2.7/dist-packages/poretools-0.5.1-py2.7.egg/poretools/poretools_main.py", line 47, in run_subtool
submodule.run(parser, args)
File "/usr/local/lib/python2.7/dist-packages/poretools-0.5.1-py2.7.egg/poretools/fastq.py", line 6, in run
for fast5 in Fast5File.Fast5FileSet(args.files):
File "/usr/local/lib/python2.7/dist-packages/poretools-0.5.1-py2.7.egg/poretools/Fast5File.py", line 36, in init
self._extract_fast5_files()
File "/usr/local/lib/python2.7/dist-packages/poretools-0.5.1-py2.7.egg/poretools/Fast5File.py", line 81, in _extract_fast5_files
shutil.rmtree(PORETOOLS_TMPDIR)
File "/usr/lib/python2.7/shutil.py", line 247, in rmtree
rmtree(fullname, ignore_errors, onerror)
File "/usr/lib/python2.7/shutil.py", line 256, in rmtree
onerror(os.rmdir, path, sys.exc_info())
File "/usr/lib/python2.7/shutil.py", line 254, in rmtree
os.rmdir(path)
OSError: [Errno 39] Directory not empty: '.poretools_tmp/H566_ON_inc'

Just need a slick way to get past the dreaded "Argument list to long." feature. Easy on some systems but horrid on OS X.

poretools fastq --type all run-2/*.fast5
-bash: /usr/local/bin/poretools: Argument list too long

Running Metrichor multiple times, e.g. with different versions will give you keys:

/Analyses/Basecall_2D_000/
/Analyses/Basecall_2D_001/
/Analyses/Basecall_2D_002/

etc.

poretools will use 000 by default and there is no way of changing this.

Therefore I think the way to handle this would be to:

1. add an option to allow the group number to be selected
2. permit a way of interrogating which groups are available in a file, and their associated Metrichor versions
3. for discussion; error out if multiple group numbers are detected in a file and no group number is specified on the command line (defaulting to 000 if there is just one group, as per current behaviour).

I am not sure if there is a way of seeing whether multiple groups are present other than querying for the existence of 001. I am also not sure if non-sequential serial numbers e.g. 000, 002 are possible.

Option to 'hist' to plot total number of bases from reads of a particular length, like MinKNOW does.

Specifically extract reads with more complement events than template events.

Would be good to move to pure Python implementation of this, and replace R dependencies with relevant Python packages. Makes it easier in particular for installing via a homebrew formula.

Trying to run occupancy, hist, or yield_plot generates a segmentation fault: 11 error on OSX.

R installed with homebrew. Poretools installed either with homebrew or python install causes the same error.

"Python quit unexpectedly while using the libR.dylib plug-in"

Process: Python [71796]
Path: /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.10 (2.7.10)
Code Type: X86-64 (Native)
Parent Process: bash [54673]
Responsible: iTerm [20335]
User ID: 501

PlugIn Path: /usr/local/Cellar/r/3.2.2_1/R.framework/Versions/3.2/Resources/lib/libR.dylib
PlugIn Identifier: libR.dylib
PlugIn Version: ??? (0)

Date/Time: 2015-11-27 17:47:37.258 -0500
OS Version: Mac OS X 10.11.1 (15B42)
Report Version: 11
Anonymous UUID: 6D2

The WIMP workflow adds an additional group Analyses/Classification_000 - this stores the taxonomic profile information. Add support to extract via poretools.

I'm getting the following error:

Traceback (most recent call last):
  File "/Users/agibiansky/poretools/env/bin/poretools", line 5, in <module>
    pkg_resources.run_script('poretools==0.2.0', 'poretools')
  File "/Users/agibiansky/poretools/env/lib/python2.7/site-packages/pkg_resources.py", line 534, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/Users/agibiansky/poretools/env/lib/python2.7/site-packages/pkg_resources.py", line 1434, in run_script
    execfile(script_filename, namespace, namespace)
  File "/Users/agibiansky/poretools/env/lib/python2.7/site-packages/poretools-0.2.0-py2.7.egg/EGG-INFO/scripts/poretools", line 4, in <module>
    import poretools.poretools_main
  File "/Users/agibiansky/poretools/env/lib/python2.7/site-packages/poretools-0.2.0-py2.7.egg/poretools/poretools_main.py", line 9, in <module>
    import stats
  File "/Users/agibiansky/poretools/env/lib/python2.7/site-packages/poretools-0.2.0-py2.7.egg/poretools/stats.py", line 2, in <module>
    import common
ImportError: No module named common

What's going on?

h5py appears (investigate this more) to have lighter dependencies and as such, may impose a slightly less onerous installation burden. Moreover, more recent versions have nice parallel computing support (http://docs.h5py.org/en/2.3/mpi.html), though it is not yet clear what benefit that would bring here.

Given a reference genome to which to align, it could be useful to provide a tool that will use LAST or LASTZ to align a run to the reference genome. Based on the alignment results, one could produce a plot compares the alignment identity to the length of the alignment. X-axis is log10(alignment length) and Y axis is %identity (50-100%). Points in the upper right quadrant are accurate, long alignments. Lower left, short, poor, etc.

As this library has fewer dependencies.

Ibid.

I sometimes have HDF5 that don't open for some reason, perhaps an incomplete file transfer. This happens often enough it might be worth having a 'quiet' mode that can skip over these duff files and carry on.

poretools stats SalmonellaRestartTraceback (most recent call last):
File "/usr/local/bin/poretools", line 5, in
pkg_resources.run_script('poretools==0.1.0', 'poretools')
File "/usr/local/lib/python2.7/dist-packages/pkg_resources.py", line 505, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/local/lib/python2.7/dist-packages/pkg_resources.py", line 1245, in run_script
execfile(script_filename, namespace, namespace)
File "/usr/local/lib/python2.7/dist-packages/poretools-0.1.0-py2.7.egg/EGG-INFO/scripts/poretools", line 5, in
poretools.poretools_main.main()
File "/usr/local/lib/python2.7/dist-packages/poretools-0.1.0-py2.7.egg/poretools/poretools_main.py", line 133, in main
args.func(parser, args)
File "/usr/local/lib/python2.7/dist-packages/poretools-0.1.0-py2.7.egg/poretools/stats.py", line 9, in run
fast5 = Fast5File.Fast5File(filename)
File "/usr/local/lib/python2.7/dist-packages/poretools-0.1.0-py2.7.egg/poretools/Fast5File.py", line 13, in init
self.open()
File "/usr/local/lib/python2.7/dist-packages/poretools-0.1.0-py2.7.egg/poretools/Fast5File.py", line 25, in open
self.hdf5file = pyhdf5.open_file(self.filename, 'r')
File "/usr/local/lib/python2.7/dist-packages/tables-3.1.1-py2.7-linux-x86_64.egg/tables/file.py", line 318, in open_file
return File(filename, mode, title, root_uep, filters, *_kwargs)
File "/usr/local/lib/python2.7/dist-packages/tables-3.1.1-py2.7-linux-x86_64.egg/tables/file.py", line 791, in init
self._g_new(filename, mode, *_params)
File "hdf5extension.pyx", line 477, in tables.hdf5extension.File._g_new (tables/hdf5extension.c:4774)
tables.exceptions.HDF5ExtError: HDF5 error back trace

File "../../../src/H5F.c", line 1514, in H5Fopen
unable to open file
File "../../../src/H5F.c", line 1309, in H5F_open
unable to read superblock
File "../../../src/H5Fsuper.c", line 305, in H5F_super_read
unable to find file signature
File "../../../src/H5Fsuper.c", line 153, in H5F_locate_signature
unable to find a valid file signature

End of HDF5 error back trace

I'm having some problems with the HDF5 dependency.

The first time I ran setup.py I got the following error message:

'''
You may need to explicitly state where your local HDF5 headers and
library can be found by setting the HDF5_DIR environment
variable or by using the --hdf5 command-line option.
'''

I have set HDF5_DIR="/usr/local/bin" as an environment variable and copied the hdf5 binaries into /usr/local/bin. But setup.py is still bombing out with the following error:

'''
/var/folders/f7/p6kh7n5j28d778t5gk89nq_m0000gn/T/easy_install-JRINep/tables-3.1.1/temp/H5closeAteKGA.c:1:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
main (int argc, char **argv) {
^~~~
/var/folders/f7/p6kh7n5j28d778t5gk89nq_m0000gn/T/easy_install-JRINep/tables-3.1.1/temp/H5closeAteKGA.c:2:5: warning: implicit declaration of function 'H5close' is invalid in C99 [-Wimplicit-function-declaration]
H5close();
^
2 warnings generated.
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
.. ERROR:: Could not find a local HDF5 installation.
You may need to explicitly state where your local HDF5 headers and
library can be found by setting the HDF5_DIR environment
variable or by using the --hdf5 command-line option.
error: Setup script exited with 1
'''

Any ideas? Thanks!

poretools should probably implement a barcode demuxing fastq extract from the fast5 files.

I have some code hacked together to do it, as well as a dataset I can volunteer if needed.

I get this bizarre error when trying to run these Poretools commands. I have a brand new macbook and have installed poretools via homebrew and via "python setup.py install".

Could the issue be the fastq_paths variable implementation in /Library/Python/2.7/site-packages/poretools-0.5.1-py2.7.egg/poretools/Fast5File.py ??

fastq_paths = {'template' : '/Analyses/Basecall_2D%03d/BaseCalled_template',
'complement' : '/Analyses/Basecall_2D_%03d/BaseCalled_complement',
'twodirections' : '/Analyses/Basecall_2D_%03d/BaseCalled_2D',
'pre_basecalled' : '/Analyses/EventDetection_000/Reads/'}_

Command and sdterr:
$ poretools hist ./
_Traceback (most recent call last):
File "/usr/local/bin/poretools", line 9, in
load_entry_point('poretools==0.5.1', 'console_scripts', 'poretools')()
File "/Library/Python/2.7/site-packages/poretools-0.5.1-py2.7.egg/poretools/poretools_main.py", line 430, in main
args.func(parser, args)
File "/Library/Python/2.7/site-packages/poretools-0.5.1-py2.7.egg/poretools/poretools_main.py", line 49, in run_subtool
submodule.run(parser, args)
File "/Library/Python/2.7/site-packages/poretools-0.5.1-py2.7.egg/poretools/hist.py", line 70, in run
fq = fast5.get_fastq()
File "/Library/Python/2.7/site-packages/poretools-0.5.1-py2.7.egg/poretools/Fast5File.py", line 296, in get_fastq
self._extract_fastqs_from_fast5(self.group)
TypeError: extract_fastqs_from_fast5() takes exactly 1 argument (2 given)

I think it probably should, otherwise if you use Fast5FileSet() in an iterator all the files will stay open. I've fixed this but just wanted to check if it is likely to cause any problems?

I noticed that there is not test data containing a full Minion run. Could you please fix this?

The events table format appears to have been changed in the current version of metrichor with the column 'raw_index' dropped. This is breaking the squiggle and events components of poretools. I.e poretools generates reads from earlier fast5 files but not those generated since at least 10th October!

Something like:

poretools events --plot foo.fast5

Can build upon the rpy2 logic now in the hist tool and build from @nickloman's wiggle.R script.

I think the header in extracted fasta files should not include the leading '@' in to be consistent with headers in exported fastq files

Current header:

>@channel_13_read_0_template

Suggested header

 >channel_13_read_0_template

Hi there,

I previously had this working but it is not working today and I have tried to reinstalled brew, hdf5 and pre tools but still get this error:

!poretools
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.4/bin/poretools", line 9, in
load_entry_point('poretools==0.5.1', 'console_scripts', 'poretools')()
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/pkg_resources/init.py", line 519, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/pkg_resources/init.py", line 2623, in load_entry_point
return ep.load()
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/pkg_resources/init.py", line 2306, in load
return self._load()
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/pkg_resources/init.py", line 2309, in _load
module = import(self.module_name, fromlist=['name'], level=0)
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/poretools-0.5.1-py3.4.egg/poretools/init.py", line 3, in
import scripts
ImportError: No module named 'scripts'

Any ideas?

After Nick helped with previous HDF5 installation problem, there was another, seems like related problem when I run poretools (run according to the ipynb). The error was:

'''
Traceback (most recent call last):
File "/Users/flashton/anaconda/bin/poretools", line 5, in
pkg_resources.run_script('poretools==0.2.0', 'poretools')
File "/Users/flashton/anaconda/lib/python2.7/site-packages/setuptools-2.2-py2.7.egg/pkg_resources.py", line 488, in run_script
File "/Users/flashton/anaconda/lib/python2.7/site-packages/setuptools-2.2-py2.7.egg/pkg_resources.py", line 1354, in run_script
File "/Users/flashton/anaconda/lib/python2.7/site-packages/poretools-0.2.0-py2.7.egg/EGG-INFO/scripts/poretools", line 3, in
import poretools.scripts
File "/Users/flashton/anaconda/lib/python2.7/site-packages/poretools-0.2.0-py2.7.egg/poretools/init.py", line 4, in
from Fast5File import *
File "/Users/flashton/anaconda/lib/python2.7/site-packages/poretools-0.2.0-py2.7.egg/poretools/Fast5File.py", line 6, in
import tables as pyhdf5
File "/Users/flashton/anaconda/lib/python2.7/site-packages/tables-3.1.1-py2.7-macosx-10.5-x86_64.egg/tables/init.py", line 82, in
from tables.utilsextension import (
ImportError: dlopen(/Users/flashton/anaconda/lib/python2.7/site-packages/tables-3.1.1-py2.7-macosx-10.5-x86_64.egg/tables/utilsextension.so, 2): Library not loaded: libhdf5.7.dylib
Referenced from: /Users/flashton/anaconda/lib/python2.7/site-packages/tables-3.1.1-py2.7-macosx-10.5-x86_64.egg/tables/utilsextension.so
Reason: image not found
'''

This is possibly related to the fact that the HDF5 from homebrew was v1.8?

e.g. my version is libhdf5.8.dylib rather than the libhdf5.7.dylib poretools seems to be expecting

To show which pores active and when

Hello,

I can't seem to python setup install due to a mismatched version with R - I have version 3.0.2, but still no go. Running Ubuntu 14.04, and I've added CRAN links to my /etc/apt/sources.list for the latest R-stuff.

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
/tmp/easy_install-iADrV_/rpy2-2.7.2/setup.py:196: UserWarning: R did not seem to have the minimum required version number
  warnings.warn("R did not seem to have the minimum required version number")
/usr/lib/R/bin/R CMD config --ldflags
/usr/lib/R/bin/R CMD config --cppflags

    Compilation parameters for rpy2's C components:
        include_dirs    = ['/usr/share/R/include']
        library_dirs    = ['/usr/lib/R/lib']
        libraries       = ['R']
        extra_link_args = []

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
warning: no files found matching 'README' anywhere in distribution
warning: no previously-included files matching '*patch*' found anywhere in distribution
warning: no previously-included files matching '*diff*' found anywhere in distribution
warning: no previously-included files matching '.hg' found anywhere in distribution
warning: no files found matching 'MANIFEST'
warning: no files found matching 'README'
warning: no files found matching 'MPL_LICENSE'
warning: no files found matching 'GPL_LICENSE'
warning: no files found matching 'LGPL_LICENSE'
no previously-included directories found matching 'dist'
warning: no files found matching 'doc/source/rpy2_logo.png'
In file included from /usr/share/R/include/Rdefines.h:25:0,
                 from ./rpy/rinterface/r_utils.c:31:
/usr/share/R/include/R_ext/Memory.h:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int R_gc_running();
 ^
In file included from /usr/share/R/include/Rdefines.h:29:0,
                 from ./rpy/rinterface/r_utils.c:31:
/usr/share/R/include/Rinternals.h:719:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 const char *R_curErrorBuf();
 ^
./rpy/rinterface/r_utils.c:32:31: fatal error: R_ext/Rallocators.h: No such file or directory
 #include <R_ext/Rallocators.h>
                               ^
compilation terminated.
error: Setup script exited with error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

As per -- perhaps an option to spit out machine-parseable output for stats too.

As per your paper (http://www.gigasciencejournal.com/content/3/1/22 - "Full 2D reads are defined as having more or equal complement events than template events") I believe the following function should return True if the number of complement events is >= (as opposed to just >) the number of template events?

def is_high_quality(self):
  if self.get_complement_events_count() > self.get_template_events_count():
    return True
  else:
    return False

To help users debug runs that are translocating too quickly, add a way of retrieving the approximate event speed by e.g. counting number of events and dividing by total duration of read.