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Request from Kiran: include PCT_TARGET_BASES_2X,PCT_TARGET_BASES_10X, 

PCT_TARGET_BASES_20X,PCT_TARGET_BASES_30X into pre-QC metrics.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5992 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-06-14 01:12:17 +00:00
parent 1fec811a47
commit 11eb74e44f
1 changed files with 8 additions and 6 deletions
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14
python/generate_per_sample_metrics.py
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@ -29,9 +29,9 @@ if not os.path.exists(sys.argv[1]):
bam_list_filename = sys.argv[1]
header = ['sample','HAPLOTYPES_CONFIDENTLY_MATCHING.MIN','HAPLOTYPES_CONFIDENTLY_MATCHING.MAX','HAPLOTYPES_CONFIDENTLY_MATCHING.MEDIAN',
'BAIT_SET','GENOME_SIZE','PCT_SELECTED_BASES','MEAN_TARGET_COVERAGE','ZERO_CVG_TARGETS_PCT','FOLD_80_BASE_PENALTY','HS_LIBRARY_SIZE',
'PCT_PF_READS_ALIGNED','PF_HQ_ERROR_RATE','MEAN_READ_LENGTH','BAD_CYCLES','STRAND_BALANCE','PCT_CHIMERAS','PCT_ADAPTER','MEDIAN_INSERT_SIZE',
'TOTAL_SNPS']
'BAIT_SET','GENOME_SIZE','PCT_SELECTED_BASES','MEAN_TARGET_COVERAGE','ZERO_CVG_TARGETS_PCT','FOLD_80_BASE_PENALTY','PCT_TARGET_BASES_2X',
'PCT_TARGET_BASES_10X','PCT_TARGET_BASES_20X','PCT_TARGET_BASES_30X','HS_LIBRARY_SIZE','PCT_PF_READS_ALIGNED','PF_HQ_ERROR_RATE',
'MEAN_READ_LENGTH','BAD_CYCLES','STRAND_BALANCE','PCT_CHIMERAS','PCT_ADAPTER','MEDIAN_INSERT_SIZE','TOTAL_SNPS']
data = ['%s'] * len(header)
print string.join(header,'\t')
@ -72,6 +72,8 @@ for sample_id,filename in samples.items():
print string.join(data,'\t')%(sample_id,min_haplotypes_confidently_matching,max_haplotypes_confidently_matching,median_haplotypes_confidently_matching,
hybrid_selection_metrics.BAIT_SET,hybrid_selection_metrics.GENOME_SIZE,hybrid_selection_metrics.PCT_SELECTED_BASES,
hybrid_selection_metrics.MEAN_TARGET_COVERAGE,hybrid_selection_metrics.ZERO_CVG_TARGETS_PCT,hybrid_selection_metrics.FOLD_80_BASE_PENALTY,
hybrid_selection_metrics.HS_LIBRARY_SIZE,alignment_summary_metrics.PCT_PF_READS_ALIGNED,alignment_summary_metrics.PF_HQ_ERROR_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)
hybrid_selection_metrics.PCT_TARGET_BASES_2X,hybrid_selection_metrics.PCT_TARGET_BASES_10X,hybrid_selection_metrics.PCT_TARGET_BASES_20X,
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.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)