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Added conditional checking for median_insert_size. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6029 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-06-22 17:59:54 +00:00
parent b35df9a0f7
commit 69f5f16711
1 changed files with 9 additions and 2 deletions
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11
python/generate_per_sample_metrics.py
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@ -78,9 +78,16 @@ for sample_id,filename in samples.items():
max_haplotypes_confidently_matching = 'NA'
median_haplotypes_confidently_matching = 'NA'
insert_size_metrics = get_metrics('%s.%s' % (basepath,'insert_size_metrics'))
if insert_size_metrics != None:
median_insert_size = insert_size_metrics[0].MEDIAN_INSERT_SIZE
else:
median_insert_size = 'NA'
hybrid_selection_metrics = get_metrics('%s.%s' % (basepath,'hybrid_selection_metrics'))[0]
alignment_summary_metrics = get_metrics('%s.%s' % (basepath,'alignment_summary_metrics'))[0]
insert_size_metrics = get_metrics('%s.%s' % (basepath,'insert_size_metrics'))[0]
dbsnp_matches = get_metrics('%s.%s' % (basepath,'dbsnp_matches'))[0]
print string.join(data,'\t')%(sample_id,min_haplotypes_confidently_matching,max_haplotypes_confidently_matching,median_haplotypes_confidently_matching,
@ -90,4 +97,4 @@ for sample_id,filename in samples.items():
hybrid_selection_metrics.PCT_TARGET_BASES_30X,hybrid_selection_metrics.HS_LIBRARY_SIZE,alignment_summary_metrics.PCT_PF_READS_ALIGNED,
alignment_summary_metrics.PF_HQ_ERROR_RATE,alignment_summary_metrics.PF_INDEL_RATE,alignment_summary_metrics.MEAN_READ_LENGTH,
alignment_summary_metrics.BAD_CYCLES,alignment_summary_metrics.STRAND_BALANCE,alignment_summary_metrics.PCT_CHIMERAS,
alignment_summary_metrics.PCT_ADAPTER,insert_size_metrics.MEDIAN_INSERT_SIZE,dbsnp_matches.TOTAL_SNPS)
alignment_summary_metrics.PCT_ADAPTER,median_insert_size,dbsnp_matches.TOTAL_SNPS)