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updated to deal with new cleaning pipeline outputs and potentially infinity TI/TV 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4098 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2010-08-24 16:01:09 +00:00
parent 25fb53e7a2
commit 83624e3af3
1 changed files with 2 additions and 2 deletions
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4
python/firehose_out_email.py
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@ -37,7 +37,7 @@ class SampSet(sample_lister.SampleSet):
ratio=dict(zip(annotations, ('','','','','')))
bpre=re.compile("all,summary,variant_counts +n bases covered +(\d+)")
size=repr(bpre.search(evalfile).group(1))
bamsearch="find /humgen/gsa-firehose/firehose/firehose_output/trunk/Sample_Set/"+self.sampset+"/* -name \*.bam"
bamsearch="find /humgen/gsa-firehose/firehose/firehose_output/trunk/Sample_Set/"+self.sampset+"/* -name \*.bam | grep -v unfixed"
bams = subprocess.Popen([bamsearch], shell=True, stdout=subprocess.PIPE).communicate()[0]
sampno=bams.count("bam")
bedsearch="find /humgen/gsa-firehose/firehose/firehose_output/trunk/Sample_Set/"+self.sampset+"/* -name \*filtered_indels.bed"
@ -46,7 +46,7 @@ class SampSet(sample_lister.SampleSet):
for a in annotations:
anregexv = re.compile(a + ",summary,variant_counts +variants +(\d+)")
variant[a] = repr(anregexv.search(evalfile).group(1))
anregexr = re.compile(a + ",summary,transitions_transversions +ratio +(\d+.\d+)")
anregexr = re.compile(a + ",summary,transitions_transversions +ratio +(\d+.\d+|Infinity)")
ratio[a] = repr(anregexr.search(evalfile).group(1))
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']
out2="\n\n\nSNP calls:"+vcf+"\n\nIndel-realigned Bam files:\n"+bams+"\nIndel calls:\n"+beds