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module for listing out samples for data processing and firehose reporting 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3847 348d0f76-0448-11de-a6fe-93d51630548a
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corin 2010-07-21 15:05:41 +00:00
parent 1209b165bf
commit 3596b1529f
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python/sample_lister.py 100755
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import os
import subprocess
#this will create a list of collaborator ids or a list of sample names--it will find cleaned bams even if they're not stored in the sample_set file system. I'm mainly using it as a module import.
class SampleSet:
def __init__(self, projectname, setname, path):
self.setname = setname
self.projectname = projectname
self.path = path
def sampslist(self):
'''finds and lists all samples in a set'''
try:
searchpath="ls /humgen/gsa-firehose/firehose/firehose_output/trunk/Sample_Set/" + self.setname +"/ -I CleanBam -I UnifiedGenotyper -I MergeBam"
raw_samps= subprocess.Popen([searchpath], shell=True, stdout=subprocess.PIPE).communicate()[0]
except IOError:
print( "Can't make sample list. Those files are not where they ought to be, or Sample_Set is not valid.")
samps = raw_samps.split("\n" + self.projectname+ "_")
samplelist = raw_samps.split("\n")[0:len(samps)]
samps[0] = samps[0].split(self.projectname+"_")[len(samps[0].split(self.projectname+"_"))-1]
samps[len(samps)-1] = samps[len(samps)-1].split("\n")[0]
return [samps, samplelist]
def bamlist(self, samplist, write=True):
'''finds and lists all cleaned bams in a sample set'''
if (write == True):
try:
if os.path.exists(self.path + "bamsfor" + self.setname + ".list"):
os.remove(self.path + "bamsfor" + self.setname + ".list")
listfile = open(self.path + "bamsfor" + self.setname + ".list", "a")
for samp in samplist:
searcher="find /humgen/gsa-firehose/firehose/firehose_output/trunk/Sample/" + repr(samp) +"/ -name \*cleaned.bam"
raw_samp= subprocess.Popen([searcher], shell=True, stdout=subprocess.PIPE).communicate()[0]
listfile.write(raw_samp)
listfile.close()
print (listfile.name)
except IOError:
print( "can't make .bam list.Those files are not where they ought to be, or Sample_Set is not valid")
else:
for samp in samplist:
searcher="find /humgen/gsa-firehose/firehose/firehose_output/trunk/Sample/" + samp +"/ -name \*cleaned.bam"
raw_samp= subprocess.Popen([searcher], shell=True, stdout=subprocess.PIPE).communicate()[0]
print(raw_samp)
def bedlist(self, samplist, write=True):
'''finds and lists all beds for a sample set'''
if (write == True):
try:
if os.path.exists(self.path + "bedsfor" + self.setname + ".list"):
os.remove(self.path + "bedsfor" + self.setname + ".list")
listfile = open(self.path + "bedsfor" + self.setname + ".list", "a")
for samp in samplist:
searcher="find /humgen/gsa-firehose/firehose/firehose_output/trunk/Sample/" + repr(samp) +"/ -name \*.bed"
raw_samp= subprocess.Popen([searcher], shell=True, stdout=subprocess.PIPE).communicate()[0]
listfile.write(raw_samp)
listfile.close()
print (listfile.name)
except IOError:
print( "can't make .bed list.Those files are not where they ought to be, or Sample_Set is not valid")
else:
for samp in samplist:
searcher="find /humgen/gsa-firehose/firehose/firehose_output/trunk/Sample/" + samp +"/ -name \*.bed"
raw_samp= subprocess.Popen([searcher], shell=True, stdout=subprocess.PIPE).communicate()[0]
print(raw_samp)
'''next two lines are example usage
#pfizer5=SampleSet("T2D_Altshuler_Pfizer_Plate_5", "T2D_Altshuler_Pfizer", "humgen/gsa-hphome1/corin/oneoffs/pfizer5/")
#pfizer5.bamlist(pfizer5.sampslist()[0], write=False)'''