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Dumb little script that grabs Picard metrics (alignment, hybrid selection, insert size) from picard_aggregation given the path to the bam file; zips them up, and spits them out; for use with Firehose 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2824 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-02-11 14:09:30 +00:00
parent a4a2c9b172
commit e491b42951
1 changed files with 13 additions and 0 deletions
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python/makeMetricsFilesForFirehose.py 100755
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#!/usr/bin/env python
import sys
import os
bam_file = sys.argv[1]
project = sys.argv[2]
directory = bam_file.rsplit("/",1)[0]+"/"
sample_id = bam_file.rsplit("/",1)[1].rsplit(".",1)[0]
is_metrics = directory+sample_id+".insert_size_metrics"
his_metrics = directory+sample_id+".hybrid_selection_metrics"
ali_metrics = directory+sample_id+".alignment_summary_metrics"
os.system("zip -j "+project+"_"+sample_id+"_sequencing_metrics"+" "+is_metrics+" "+his_metrics+" "+ali_metrics)