diff --git a/python/firehose_out_email.py b/python/firehose_out_email.py index 3ebb7e96d..3e06420fc 100755 --- a/python/firehose_out_email.py +++ b/python/firehose_out_email.py @@ -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