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fixed silly syntax errors 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3805 348d0f76-0448-11de-a6fe-93d51630548a
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corin 2010-07-16 15:08:46 +00:00
parent 917469ef43
commit 74f705d943
1 changed files with 3 additions and 6 deletions
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9
python/firehose_out_email.py
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@ -3,7 +3,7 @@ import os
import re import re
import sample_lister import sample_lister
class SampSet(sample_lister.SampleSet) class SampSet(sample_lister.SampleSet):
def __init__(self, sampset, pathname): def __init__(self, sampset, pathname):
self.sampset=sampset self.sampset=sampset
self.pathname=pathname self.pathname=pathname
@ -21,15 +21,12 @@ class SampSet(sample_lister.SampleSet)
anregexv = re.compile(a + ",summary,variant_counts +variants +(\d+)") anregexv = re.compile(a + ",summary,variant_counts +variants +(\d+)")
variant[a] = repr(anregexv.search(evalfile).group(1)) 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+)")
print (anregexr.search(evalfile)) ratio[a] = repr(anregexr.search(evalfile).group(1)
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'] ) 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=SampSet("EOMI_Kathiresan_NHGRI", "test")
#EOMI.evalout() <-this and the line above are examples #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. #TODO: make this find the list of bams, bed files, and annotated vcfs.