| Previous changeset 8:f5a8d626a329 (2012-10-08) |
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Commit message:
Uploaded |
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added:
checkSnpEffCandidates.py |
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| diff -r f5a8d626a329 -r f20585ccbf05 checkSnpEffCandidates.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/checkSnpEffCandidates.py Mon Oct 08 16:14:46 2012 -0400 |
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| @@ -0,0 +1,70 @@ +#!/usr/bin/python + +import sys +import optparse +import csv +import re + +def main(): + parser = optparse.OptionParser() + parser.add_option('-s', '--snpeff_file', dest = 'snpeff_file', action = 'store', type = 'string', default = None, help = "Path to the snpEff file") + parser.add_option('-c', '--candidate_list', dest = 'candidate_list', action = 'store', type = 'string', default = None, help = "Two column tabular list of candidate Gene ID, Type") + parser.add_option('-o', '--output', dest = 'output', action = 'store', type = 'string', default = None, help = "Output file name") + (options, args) = parser.parse_args() + + snpeff_file = options.snpeff_file + candidate_list = options.candidate_list + + candidates = parse_candidate_list(candidate_list = candidate_list) + mark_snpeff_file(snpeff_file = snpeff_file, output = options.output, candidates = candidates) + +def skip_and_write_headers(writer = None, reader = None, i_file = None): + # count headers + comment = 0 + while reader.next()[0].startswith('#'): + comment = comment + 1 + + # skip and write headers + i_file.seek(0) + for i in range(0, comment): + row = reader.next() + writer.writerow(row) + +def parse_candidate_list(candidate_list = ""): + i_file = open(candidate_list, 'rU') + reader = csv.reader(i_file, delimiter = '\t',) + + candidates = {} + for row in reader: + gene_id = row[0] + gene_type = row[1] + candidates[gene_id] = gene_type + + i_file.close() + + return candidates + +def mark_snpeff_file(snpeff_file = "", output = "", candidates = None): + i_file = open(snpeff_file, 'rU') + reader = csv.reader(i_file, delimiter = '\t') + + o_file = open(output, 'wb') + writer = csv.writer(o_file, delimiter = '\t') + + skip_and_write_headers(writer = writer, reader = reader, i_file = i_file) + + for row in reader: + gene_id = row[9] + if gene_id in candidates: + gene_type = candidates[gene_id] + row.append(gene_type) + else: + row.append('') + + writer.writerow(row) + + o_file.close() + i_file.close() + +if __name__ == "__main__": + main() |