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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
This commit is contained in:
andrewk 2009-12-16 18:06:08 +00:00
parent e051311e8c
commit bf76019f22
1 changed files with 3 additions and 2 deletions
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5
python/CoverageEval.py
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@ -221,7 +221,7 @@ def stats_from_hist(options, depth_hist_filename, stats_filename, variant_eval_d
hist = [] 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): for index, record in enumerate(hist_gen):
assert int(record["depth"]) == index assert int(record["depth"]) == index
hist.append(int(record["count"])) 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 total_predicted += predicted
perfect = prob_genotype[genotype.index]*total_hist_sites perfect = prob_genotype[genotype.index]*total_hist_sites
diff = perfect - predicted 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) #repl_string += "%s %.0f\n" % (genotype, predicted)
print " Total calls: %7d" % total_predicted print " Total calls: %7d" % total_predicted