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Adding this to get around lsf/csh issues (see recent help message). Also seems like a good time to reiterate http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/ 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4309 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-09-19 02:45:16 +00:00
parent c6351a11d6
commit fa8cfd3031
3 changed files with 21 additions and 10 deletions
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20
python/gatherIndelsToVCF.py
View File

@ -5,7 +5,6 @@ import sys
input_verbose_beds = sys.argv[1].split(",") input_verbose_beds = sys.argv[1].split(",")
output_vcf_name = sys.argv[2] output_vcf_name = sys.argv[2]
reference_file = sys.argv[3]
vcf_header = ["#CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"] vcf_header = ["#CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
format = "GT:FT" format = "GT:FT"
@ -119,11 +118,13 @@ def fixAlts(alts_in):
return ",".join(fixed_alts) return ",".join(fixed_alts)
def fixChrom(chrom): def fixChrom(chrom):
if ( chrom == 0 ):
return "chrM")
if ( chrom == "23" ): if ( chrom == "23" ):
return "X" return "chrX"
if ( chrom == "24" ): if ( chrom == "24" ):
return "Y" return "chrY"
return chrom return "chr"+chrom
def writeVCFLine(out_stream,indel_list,sample_list): def writeVCFLine(out_stream,indel_list,sample_list):
alts = getAlts(indel_list) alts = getAlts(indel_list)
@ -175,10 +176,13 @@ def parseIndels(filePath,sampleName):
for line in f.readlines(): for line in f.readlines():
if ( not line.startswith("[") ): if ( not line.startswith("[") ):
spline = line.split("\t") spline = line.split("\t")
if ( spline[0] != "X" and spline[0] != "Y" ): spline[0] = spline[0].split("chr")[1]
if ( spline[0] != "X" and spline[0] != "Y" and spline[0] != "M"):
chrom = int(spline[0]) chrom = int(spline[0])
else: else:
if ( spline[0] == "X"): if ( spline[0] == "M" ):
chrom = 0
elif ( spline[0] == "X"):
chrom = 23 chrom = 23
else: else:
chrom = 24 chrom = 24
@ -225,7 +229,3 @@ def writeVCF(verbose_bed_list):
writeVCF(input_verbose_beds) writeVCF(input_verbose_beds)
## now dumb hacky thing
cmd = "java -jar /humgen/gsa-scr1/chartl/sting/dist/GenomeAnalysisTK.jar -T VCFReferenceFixer -B fixme,VCF,"+output_vcf_name+"_BAD_REFERENCE.vcf -o "+output_vcf_name+" -R "+reference_file+" -l INFO"
os.system(cmd)

10
python/lsf_post_touch.py 100755
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@ -0,0 +1,10 @@
import sys
import os
status = sys.argv[1]
directories = list()
for j in range(2,len(sys.argv)) :
directories.append(sys.argv[j])
if ( status == "0" ):
os.system("touch "+" ".join(directories))

1
python/splitIntervalsByContig.py
View File

@ -1,3 +1,4 @@
#!/usr/bin/python
import sys import sys
input_file = sys.argv[1] input_file = sys.argv[1]
file_index = 1 file_index = 1