64 lines
3.4 KiB
Python
Executable File
64 lines
3.4 KiB
Python
Executable File
#this script produces the output to go in emails
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import subprocess
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import os
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import re
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import sys
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import getopt
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import sample_lister
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try:
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opts, args = getopt.getopt(sys.argv[1:], "dp:s:")
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except getopt.GetoptError, err:
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# print help information and exit:
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print str(err) # will print something like "option -a not recognized"
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usage()
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sys.exit(2)
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opts=dict(opts)
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givenname=opts['-s']
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projname=opts['-p']
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if '-d' in opts:
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dirname=opts['-d']
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else:
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dirname=""
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class SampSet(sample_lister.SampleSet):
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def __init__(self, projectname, sampset, pathname):
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self.sampset=sampset
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self.pathname=pathname
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self.projectname=projectname
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sample_lister.SampleSet.__init__(self, projectname, sampset, pathname)
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def evalout(self):
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'''This produced the output that needs to go in the emails'''
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filename = "/humgen/gsa-firehose/firehose/firehose_output/trunk/Sample_Set/" + self.sampset +"/UnifiedGenotyper/"+ self.sampset+".filtered.eval"
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evalfile = open(filename, "r").read()
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annotations= ["all", "novel", "known", "snp_at_known_non_snps", "filtered"]
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variant=dict(zip(annotations, ('','','','','')))
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ratio=dict(zip(annotations, ('','','','','')))
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bpre=re.compile("all,summary,variant_counts +n bases covered +(\d+)")
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size=repr(bpre.search(evalfile).group(1))
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bamsearch="find /humgen/gsa-firehose/firehose/firehose_output/trunk/Sample_Set/"+self.sampset+"/* -name \*.bam | grep -v unfixed"
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bams = subprocess.Popen([bamsearch], shell=True, stdout=subprocess.PIPE).communicate()[0]
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sampno=bams.count("bam")
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bedsearch="find /humgen/gsa-firehose/firehose/firehose_output/trunk/Sample_Set/"+self.sampset+"/* -name \*filtered_indels.bed"
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beds = subprocess.Popen([bedsearch], shell=True, stdout=subprocess.PIPE).communicate()[0]
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vcf="/humgen/gsa-firehose/firehose/firehose_output/trunk/Sample_Set/"+self.sampset+"/UnifiedGenotyper/"+self.sampset+'.maf.annotated.vcf'
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for a in annotations:
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anregexv = re.compile(a + ",summary,variant_counts +variants +(\d+)")
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variant[a] = repr(anregexv.search(evalfile).group(1))
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anregexr = re.compile(a + ",summary,transitions_transversions +ratio +(\d+.\d+|Infinity)")
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ratio[a] = repr(anregexr.search(evalfile).group(1))
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out1="Samples processed:"+repr(sampno)+"\n\n Target size: \t" +size+" bp \n\n\t\t\t\t\t Variants \t\t Ti/TV \n (true positives)\t All \t\t " +variant["all"]+ " \t\t " + ratio["all"] +" \n \t\t\t Known \t\t " +variant["known"]+ " \t\t " + ratio['known']+" \n \t\t\t Novel \t\t " +variant["novel"]+" \t\t " + ratio['novel']+ " \n*************************************************************************\n (false \tSNPS at known indels \t " +variant["snp_at_known_non_snps"]+"\t\t\t " + ratio['snp_at_known_non_snps']+ " \n positives) \t\t filtered \t " +variant["filtered"]+" \t\t " + ratio['filtered']
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out2="\n\n\nSNP calls:"+vcf+"\n\nIndel-realigned Bam files:\n"+bams+"\nIndel calls:\n"+beds
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if self.pathname == '':
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print(out1+out2)
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else:
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filename=self.pathname+self.sampset+".emailtxt"
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putthere=open(filename, "w")
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putthere.write(out1+out2)
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target=SampSet(projname,givenname,dirname)
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target.evalout()
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#TODO: make this send the email when run
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#TODO: make this find the list of bams, bed files, and annotated vcfs.
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