Last active
August 10, 2016 20:01
-
-
Save sxv/3dbc1c561b1d15e60a35 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import sys | |
| from glob import glob | |
| if (len(sys.argv)<=1): match = '*n0*' | |
| else: match = sys.argv[1] | |
| file = glob(match)[0] | |
| counts = {} | |
| with open(file) as f: | |
| print f.readline() | |
| for line in f: | |
| gene = line.split("\t")[7] | |
| case = line.split("\t")[0] | |
| if gene in counts: | |
| if case not in counts[gene]: counts[gene].append(case) | |
| else: counts[gene] = [case] | |
| for gene in sorted(counts, key = lambda gene: len(counts[gene]), reverse=True): | |
| # if len(counts[gene]) < 2: break | |
| group = [] | |
| for line in open(file): | |
| if line.split("\t")[7] == gene: | |
| group.append(line) | |
| lines = '' | |
| cases = [] | |
| dups = [] | |
| noise = 0 | |
| for line in sorted(group, key = lambda x: (x.split("\t")[1], x.split("\t")[2])): | |
| case = line.split("\t")[0] | |
| if case in cases: | |
| if case not in dups: | |
| dups.append(case) | |
| noise += 1 # another one bites the dust | |
| else: cases.append(case) | |
| lines += line | |
| print "%s has %s variants from %s cases (%s cases have exactly 1 variant in this gene)" \ | |
| % (gene, len(group), len(set(cases)), len(set(cases))-noise) | |
| print lines |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment