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Merged
rhshah merged 3 commits into from
Apr 3, 2017
Merged

Merge From Master #3

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d18fc75
Adding Proper Versioning in setup.py
rhshah Apr 3, 2017
141c7ea
Bug fixes
rhshah Apr 3, 2017
66f579b
Bug Fixes
rhshah Apr 3, 2017
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2 changes: 1 addition & 1 deletion Makefile
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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,4 +2,4 @@ init:
pip install -r requirements.txt

test:
nosetests tests
nosetests -v --with-coverage --cover-tests tests
1 change: 1 addition & 0 deletions mutect/filter_mutect.py
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@@ -1,3 +1,4 @@
#!/usr/bin/python
'''
@Description : This tool helps to filter muTect v1.14 txt and vcf through command line.
@Created : 07/17/2016
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2 changes: 1 addition & 1 deletion mutect/outputs.yaml
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Expand Up@@ -16,4 +16,4 @@ outputs:
if (inputs.inputTxt)
return inputs.inputTxt.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
return null;
}
}
10 changes: 5 additions & 5 deletions mutect/postprocess.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@

import argparse
import ruamel.yaml

import os

def read(filename):
"""return file contents"""
Expand DownExpand Up@@ -33,14 +33,14 @@ def main():
)

params = parser.parse_args()

dir_path = os.path.dirname(os.path.realpath(__file__))
cwl = ruamel.yaml.load(read(params.filename_cwl),
ruamel.yaml.RoundTripLoader)

script_path = os.path.join(dir_path,'filter_mutect.py')
cwl['baseCommand'] = ['python',script_path]
cwl['inputs']['inputVcf']['type'] = ['string', 'File']
cwl['inputs']['inputTxt']['type'] = ['string', 'File']
cwl['inputs']['hotspotVcf']['type'] = ['string', 'File']
cwl['inputs']['version']['default'] = 'default'
cwl['inputs']['hotspotVcf']['type'] = ['null','string', 'File']

write(params.filename_cwl, ruamel.yaml.dump(
cwl, Dumper=ruamel.yaml.RoundTripDumper))
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1 change: 1 addition & 0 deletions pindel/filter_pindel.py
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@@ -1,3 +1,4 @@
#!/usr/bin/python
"""
@Description : This tool helps to filter pindel v0.2.5a7 vcf through command line.
@Created : 07/17/2014
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2 changes: 1 addition & 1 deletion pindel/outputs.yaml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -16,4 +16,4 @@ outputs:
if (inputs.inputVcf)
return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
return null;
}
}
10 changes: 6 additions & 4 deletions pindel/postprocess.py
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Expand Up@@ -3,7 +3,7 @@

import argparse
import ruamel.yaml

import os

def read(filename):
"""return file contents"""
Expand DownExpand Up@@ -33,13 +33,15 @@ def main():
)

params = parser.parse_args()

dir_path = os.path.dirname(os.path.realpath(__file__))
cwl = ruamel.yaml.load(read(params.filename_cwl),
ruamel.yaml.RoundTripLoader)

script_path = os.path.join(dir_path,'filter_pindel.py')
cwl['baseCommand'] = ['python',script_path]
cwl['inputs']['inputVcf']['type'] = ['string', 'File']
cwl['inputs']['hotspotVcf']['type'] = ['string', 'File']
cwl['inputs']['version']['default'] = 'default'
cwl['inputs']['hotspotVcf']['type'] = ['null', 'string', 'File']


write(params.filename_cwl, ruamel.yaml.dump(
cwl, Dumper=ruamel.yaml.RoundTripDumper))
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up@@ -11,7 +11,7 @@

setup(
name='basicfiltering',
version='0.1.0',
version='0.1.3',
description='Package for filtering multiple variant calling tools',
long_description=readme,
author='Ronak Shah',
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1 change: 1 addition & 0 deletions somaticindeldetector/filter_sid.py
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@@ -1,3 +1,4 @@
#!/usr/bin/python
'''
@Description : This tool helps to filter SomaticIndelDetector vcf and txt through command line.GATK version: 2.3-9
@Created : 07/25/2016
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2 changes: 1 addition & 1 deletion somaticindeldetector/outputs.yaml
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Expand Up@@ -16,4 +16,4 @@ outputs:
if (inputs.inputVcf)
return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
return null;
}
}
9 changes: 5 additions & 4 deletions somaticindeldetector/postprocess.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@

import argparse
import ruamel.yaml

import os

def read(filename):
"""return file contents"""
Expand DownExpand Up@@ -33,14 +33,15 @@ def main():
)

params = parser.parse_args()

dir_path = os.path.dirname(os.path.realpath(__file__))
cwl = ruamel.yaml.load(read(params.filename_cwl),
ruamel.yaml.RoundTripLoader)

script_path = os.path.join(dir_path,'filter_sid.py')
cwl['baseCommand'] = ['python',script_path]
cwl['inputs']['inputVcf']['type'] = ['string', 'File']
cwl['inputs']['inputTxt']['type'] = ['string', 'File']
cwl['inputs']['hotspotVcf']['type'] = ['string', 'File']
cwl['inputs']['version']['default'] = 'default'
cwl['inputs']['hotspotVcf']['type'] = ['null', 'string', 'File']

write(params.filename_cwl, ruamel.yaml.dump(
cwl, Dumper=ruamel.yaml.RoundTripDumper))
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1 change: 1 addition & 0 deletions vardict/filter_vardict.py
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Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
#!/usr/bin/python
'''
@Description : This tool helps to filter vardict vcf through command line for version 1.4.6
@Created : 04/22/2016
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2 changes: 1 addition & 1 deletion vardict/outputs.yaml
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Expand Up@@ -16,4 +16,4 @@ outputs:
if (inputs.inputVcf)
return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
return null;
}
}
9 changes: 5 additions & 4 deletions vardict/postprocess.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@

import argparse
import ruamel.yaml

import os

def read(filename):
"""return file contents"""
Expand DownExpand Up@@ -33,13 +33,14 @@ def main():
)

params = parser.parse_args()

dir_path = os.path.dirname(os.path.realpath(__file__))
cwl = ruamel.yaml.load(read(params.filename_cwl),
ruamel.yaml.RoundTripLoader)

script_path = os.path.join(dir_path,'filter_vardict.py')
cwl['baseCommand'] = ['python',script_path]
cwl['inputs']['inputVcf']['type'] = ['string', 'File']
cwl['inputs']['hotspotVcf']['type'] = ['string', 'File']
cwl['inputs']['version']['default'] = 'default'
cwl['inputs']['hotspotVcf']['type'] = ['null', 'string', 'File']

write(params.filename_cwl, ruamel.yaml.dump(
cwl, Dumper=ruamel.yaml.RoundTripDumper))
Expand Down