From 69f5f1671190e9bc096d8eb06a8a1d97bd535e9c Mon Sep 17 00:00:00 2001 From: kshakir Date: Wed, 22 Jun 2011 17:59:54 +0000 Subject: [PATCH] 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 --- python/generate_per_sample_metrics.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/python/generate_per_sample_metrics.py b/python/generate_per_sample_metrics.py index 0b821521e..7c101b82a 100644 --- a/python/generate_per_sample_metrics.py +++ b/python/generate_per_sample_metrics.py @@ -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)