Merging from Master

README.md

@@ -12,7 +12,7 @@ for Multiple Tools
 [![codecov](https://codecov.io/gh/rhshah/basicfiltering/branch/master/graph/badge.svg)](https://codecov.io/gh/rhshah/basicfiltering)
 
 ## Requirements:
-- pyvcf : [v0.6.8](http://pyvcf.readthedocs.io/en/latest/INTRO.html)
+- pyvcf : [v0.6.7](http://pyvcf.readthedocs.io/en/latest/INTRO.html)
 - pandas : [v0.16.2](http://pandas.pydata.org/)
 - nose : [v1.3.7](http://nose.readthedocs.io/en/latest/)
 

data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.vcf

@@ -13,6 +13,7 @@
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Reference depth, how many reads support the reference">
 ##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Allele depth, how many reads support this allele">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total coverage at the site">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	PoolNormal-N	PoolTumor2-T
 2	6636086	.	A	AGCTTCGTTAAACTTCACTCGGAAGT	.	PASS	END=6636086;HOMLEN=0;SVLEN=25;SVTYPE=INS	GT:AD	0/0:554,1	0/0:719,10
 2	29451557	.	GAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC	G	.	PASS	END=29451604;HOMLEN=7;HOMSEQ=AGGCAGG;SVLEN=-47;SVTYPE=DEL	GT:AD	0/0:59,0	0/0:145,5

mutect/filter_mutect.py

@@ -2,7 +2,7 @@
 '''
 @Description : This tool helps to filter muTect v1.14 txt and vcf through command line. 
 @Created :  07/17/2016
-@Updated : 03/17/2017
+@Updated : 04/18/2017
 @author : Ronak H Shah
 
 '''
@@ -26,6 +26,7 @@
     pass
 try:
     import vcf
+    from vcf.parser import _Info as VcfInfo, field_counts as vcf_field_counts
 except ImportError:
     logger.fatal("filter_mutect: pyvcf is not installed, please install pyvcf as it is required to run the mapping.")
     sys.exit(1)
@@ -68,6 +69,7 @@ def RunStdFilter(args):
         vcf_out = vcf_out + "_STDfilter.vcf"
         txt_out = txt_out + "_STDfilter.txt"
     vcf_reader = vcf.Reader(open(args.inputVcf, 'r'))   
+    vcf_reader.infos['FAILURE_REASON'] = VcfInfo('FAILURE_REASON', '1', 'String', 'Failure Reason from MuTect text File')
     vcf_writer = vcf.Writer(open(vcf_out, 'w'), vcf_reader)
     txtDF = pd.read_table(args.inputTxt, skiprows=1, low_memory=False)
     txt_fh = open(txt_out, "wb") 
@@ -149,6 +151,10 @@ def RunStdFilter(args):
     for record in vcf_reader:
         key_for_tracking = str(record.CHROM) + ":" + str(record.POS) + ":" + str(record.REF) + ":" + str(record.ALT[0]) 
         if(key_for_tracking in keepDict):
+            failure_reason = keepDict.get(key_for_tracking)
+            if(failure_reason == "KEEP"):
+                failure_reason = "None"
+            record.add_info('FAILURE_REASON', failure_reason)
             if(record.FILTER == "PASS"):
 
                 vcf_writer.write_record(record)

pindel/filter_pindel.py

@@ -2,7 +2,7 @@
 """
 @Description : This tool helps to filter pindel v0.2.5a7 vcf through command line. 
 @Created :  07/17/2014
-@Updated: 03/17/2017
+@Updated: 04/18/2017
 @author : Ronak H Shah
 
 """
@@ -26,6 +26,7 @@
     pass
 try:
     import vcf
+    from vcf.parser import _Format as VcfFormat, field_counts as vcf_field_counts
 except ImportError:
     logger.fatal("filter_pindel: pyvcf is not installed, please install pyvcf as it is required to run the mapping.")
     sys.exit(1)
@@ -157,6 +158,7 @@ def RunStdFilter(args):
         vcf_out = vcf_out + "_STDfilter.vcf"
         txt_out = txt_out + "_STDfilter.txt"
     vcf_reader = vcf.Reader(open(args.inputVcf, 'r'))
+    vcf_reader.formats['DP'] = VcfFormat('DP', '1', 'Integer', 'Total coverage at the site')
     vcf_writer = vcf.Writer(open(vcf_out, 'w'), vcf_reader)
     txt_fh = open(txt_out, "wb")
     allsamples = vcf_reader.samples

requirements.txt

@@ -1,5 +1,5 @@
 nose==1.3.7
-pyvcf==0.6.8
+pyvcf==0.6.7
 pandas==0.16.2
 coloredlogs==5.2
 codecov==2.0.5

setup.py

@@ -11,7 +11,7 @@
 
 setup(
     name='basicfiltering',
-    version='0.1.3',
+    version='0.1.4',
     description='Package for filtering multiple variant calling tools',
     long_description=readme,
     author='Ronak Shah',