From e491b42951af93429458cc7b5c5d3e8a61a2e3f1 Mon Sep 17 00:00:00 2001 From: chartl Date: Thu, 11 Feb 2010 14:09:30 +0000 Subject: [PATCH] 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 --- python/makeMetricsFilesForFirehose.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100755 python/makeMetricsFilesForFirehose.py diff --git a/python/makeMetricsFilesForFirehose.py b/python/makeMetricsFilesForFirehose.py new file mode 100755 index 000000000..e13d8d1fc --- /dev/null +++ b/python/makeMetricsFilesForFirehose.py @@ -0,0 +1,13 @@ +#!/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)