diff --git a/python/firehose_out_email.py b/python/firehose_out_email.py new file mode 100755 index 000000000..b2c6700f6 --- /dev/null +++ b/python/firehose_out_email.py @@ -0,0 +1,35 @@ +#this script produces the output to go in emails +import os +import re +import sample_lister + +class SampSet(sample_lister.SampleSet) + def __init__(self, sampset, pathname): + self.sampset=sampset + self.pathname=pathname + sample_lister.SampleSet.__init__(self, sampset, pathname) + def evalout(self): + '''This produced the output that needs to go in the emails''' + filename = "/humgen/gsa-firehose/firehose/firehose_output/trunk/Sample_Set/" + self.sampset +"/UnifiedGenotyper/"+ self.sampset+".filtered.eval" + evalfile = open(filename, "r").read() + annotations= ["all", "novel", "known", "snp_at_known_non_snps", "filtered"] + variant=dict(zip(annotations, ('','','','',''))) + ratio=dict(zip(annotations, ('','','','',''))) + bpre=re.compile("all,summary,variant_counts +n bases covered +(\d+)") + size=repr(bpre.search(evalfile).group(1)) + 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+)") + print (anregexr.search(evalfile)) + ratio[a] = repr(anregexr.search(evalfile).group(1)) + print (a) + print (ratio[a]) + print("Samples processed:\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'] ) + + +#EOMI=SampSet("EOMI_Kathiresan_NHGRI", "test") +#EOMI.evalout() <-this and the line above are examples + +#TODO: make this send the email when run +#TODO: make this find the list of bams, bed files, and annotated vcfs.