From 11eb74e44fd004447adbaad34cec5bc1f87b839b Mon Sep 17 00:00:00 2001 From: hanna Date: Tue, 14 Jun 2011 01:12:17 +0000 Subject: [PATCH] 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 --- python/generate_per_sample_metrics.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/python/generate_per_sample_metrics.py b/python/generate_per_sample_metrics.py index d24948c30..8dddf8233 100644 --- a/python/generate_per_sample_metrics.py +++ b/python/generate_per_sample_metrics.py @@ -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)