From bf76019f228f7f506b56987d8ca46425d21ade87 Mon Sep 17 00:00:00 2001 From: andrewk Date: Wed, 16 Dec 2009 18:06:08 +0000 Subject: [PATCH] Minor change to coverage evalution script, to update for new file format and add output fields git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2375 348d0f76-0448-11de-a6fe-93d51630548a --- python/CoverageEval.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/python/CoverageEval.py b/python/CoverageEval.py index 2c15f6b10..98bf1272d 100755 --- a/python/CoverageEval.py +++ b/python/CoverageEval.py @@ -221,7 +221,7 @@ def stats_from_hist(options, depth_hist_filename, stats_filename, variant_eval_d hist = [] - hist_gen = FlatFileTable.record_generator(depth_hist_filename, sep=" ", skip_n_lines=3) + hist_gen = FlatFileTable.record_generator(depth_hist_filename, sep=" ", skip_n_lines=9) for index, record in enumerate(hist_gen): assert int(record["depth"]) == index hist.append(int(record["count"])) @@ -290,7 +290,8 @@ def stats_from_hist(options, depth_hist_filename, stats_filename, variant_eval_d total_predicted += predicted perfect = prob_genotype[genotype.index]*total_hist_sites diff = perfect - predicted - print "%19s calls: %7.0f %7.0f %7.0f" % (genotype, predicted, perfect, diff) + percent_of_possible = predicted / perfect * 100 + print "%19s calls: %8.0f %8.0f %8.0f %8.1f" % (genotype, predicted, perfect, diff, percent_of_possible) #repl_string += "%s %.0f\n" % (genotype, predicted) print " Total calls: %7d" % total_predicted