j35p312 / amycne Goto Github PK
View Code? Open in Web Editor NEWA copy number estimation toolkit
amycne's Issues
Calculators FFY and FFX
Hi
I have looked at the code to calculate FFY and FFX, but I don't quite understand how to calculate it. Can you describe in detail how it is calculated?
UnboundLocalError: local variable 'region' referenced before assignment
Trying to use the program returns the error in the title. The cause appears to be in genotype.py at line 40:
def main(Data,GC_hist,args):
#get the coverage across the region
coverage_list=[]
len_list=[]
gc_list=[]
ref_list=[]
total_bin_list=[]
bin_count = 0
used_bin_count = 0
operations=[]
if args.region:
for line in open(args.region):
mode,regions = retrieve_regions(line)
operations.append({"mode": mode, "regions":regions,"command":line.strip()})
else:
chromosome=region.split(":")[0]
The chromosome=region.split(":")[0] line fails because it calls region (which has not been defined yet) rather than args.region as it's likely meant to.
Edit: It should be args.R not args.region.
Problems with reproduction of AMY1 test
Hello,
I've been trying to execute the following line:
python AMYCNE.py --genotype --gc ref_gc_cont.tab --coverage jap_hum_cov.tab --region AMY1.txt --Q 0
I'm using the AMY1.txt file provided by the documentation and gc and coverage tables were generated with TIDDIT and Generate_GC_tab.py The gc table was generated using the human reference genome ch38. The coverage tab was generated from the file HGDP00772.alt_bwamem_GRCh38DH.20181023.Japanese.cram colected from HGDP converted to .bam with samtools.
I receive the following error message:
Error: Too many low quality regions! consider rerunning the analysis using a smaller --size_cutoff, and less strict regions masking
I tried using the optional argument --s_cutoff with the values 10, 1 and 0 and still got the same message
Is there a value that you could recommed? Or a better .bam file to run this test?
Thank you in advance,
Luiza Gomes
Problem with create file GC_content.tab
Predicting fetal fraction
Hello,
how to predict fetal fraction using python AMYCNE.py --ff ? What files should I use for predicting fetal fraction? Please let me know.
Just tried AMYCNE, stack trace after a while
I get this stack output:
I mapped data to grch38 (the full set, including alt contigs etc.)
I used sambamba depth to generate the coverage file and your GC script for the GC tsv file.
example input:
$head ref_gc.tsv
1 0 100 -1.0
1 100 200 -1.0
1 200 300 -1.0
1 300 400 -1.0
1 400 500 -1.0
1 500 600 -1.0
1 600 700 -1.0
1 700 800 -1.0
1 800 900 -1.0
1 900 1000 -1.0
$ tail ref_gc.tsv
HLA-DRB1*16:02:01 10100 10200 0.4
HLA-DRB1*16:02:01 10200 10300 0.4
HLA-DRB1*16:02:01 10300 10400 0.52
HLA-DRB1*16:02:01 10400 10500 0.53
HLA-DRB1*16:02:01 10500 10600 0.38
HLA-DRB1*16:02:01 10600 10700 0.52
HLA-DRB1*16:02:01 10700 10800 0.45
HLA-DRB1*16:02:01 10800 10900 0.49
HLA-DRB1*16:02:01 10900 11000 0.55
HLA-DRB1*16:02:01 11000 11005 0.2
$ head Y2_6pg_13_cycles.md.even_cov.cov
# chrom chromStart chromEnd readCount meanCoverage sampleName
1 16400 16500 1 0.7 Y2_6pg_13_cycles
1 16500 16600 2 0.63 Y2_6pg_13_cycles
1 16600 16700 1 0.17 Y2_6pg_13_cycles
1 16700 16800 0 0 Y2_6pg_13_cycles
1 16800 16900 0 0 Y2_6pg_13_cycles
1 16900 17000 0 0 Y2_6pg_13_cycles
1 17000 17100 0 0 Y2_6pg_13_cycles
1 17100 17200 0 0 Y2_6pg_13_cycles
1 17200 17300 0 0 Y2_6pg_13_cycles
$ tail Y2_6pg_13_cycles.md.even_cov.cov
HLA-DRB1*16:02:01 10000 10100 0 0 Y2_6pg_13_cycles
HLA-DRB1*16:02:01 10100 10200 0 0 Y2_6pg_13_cycles
HLA-DRB1*16:02:01 10200 10300 0 0 Y2_6pg_13_cycles
HLA-DRB1*16:02:01 10300 10400 0 0 Y2_6pg_13_cycles
HLA-DRB1*16:02:01 10400 10500 0 0 Y2_6pg_13_cycles
HLA-DRB1*16:02:01 10500 10600 0 0 Y2_6pg_13_cycles
HLA-DRB1*16:02:01 10600 10700 0 0 Y2_6pg_13_cycles
HLA-DRB1*16:02:01 10700 10800 0 0 Y2_6pg_13_cycles
HLA-DRB1*16:02:01 10800 10900 0 0 Y2_6pg_13_cycles
HLA-DRB1*16:02:01 10900 11000 0 0 Y2_6pg_13_cycles
Command output:
finished reading the coverage data
applying filters
computing coverage histogram
Command error:
/mnt/flash_scratch/nextflow_conda/env-4731703d9d1e13495b9cb3da6a63e29e/lib/python2.7/site-packages/numpy/core/fromnumeric.py:3118: RuntimeWarning: Mean of empty slice.
out=out, **kwargs)
/mnt/flash_scratch/nextflow_conda/env-4731703d9d1e13495b9cb3da6a63e29e/lib/python2.7/site-packages/numpy/core/_methods.py:85: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
Traceback (most recent call last):
File "...bin/AMYCNE.py", line 164, in <module>
call.main(Data,GC_hist,args)
File "call.py", line 338, in call.main
ratio_hist=chromosome_hist(Data,args.Q)
File "call.py", line 156, in call.chromosome_hist
for chromosome in Data["chromosomes"]:
TypeError: list indices must be integers, not str
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.