diff --git a/python/firehose_out_email.py b/python/firehose_out_email.py index b2c6700f6..ff799f26b 100755 --- a/python/firehose_out_email.py +++ b/python/firehose_out_email.py @@ -3,7 +3,7 @@ import os import re import sample_lister -class SampSet(sample_lister.SampleSet) +class SampSet(sample_lister.SampleSet): def __init__(self, sampset, pathname): self.sampset=sampset self.pathname=pathname @@ -21,15 +21,12 @@ class SampSet(sample_lister.SampleSet) 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]) + ratio[a] = repr(anregexr.search(evalfile).group(1) 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 send the email when run with a setname as input #TODO: make this find the list of bams, bed files, and annotated vcfs.