Mercurial > repos > miller-lab > genome_diversity
diff diversity_pi.py @ 27:8997f2ca8c7a
Update to Miller Lab devshed revision bae0d3306d3b
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Mon, 15 Jul 2013 10:47:35 -0400 |
parents | 248b06e86022 |
children | a631c2f6d913 |
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--- a/diversity_pi.py Mon Jun 03 12:29:29 2013 -0400 +++ b/diversity_pi.py Mon Jul 15 10:47:35 2013 -0400 @@ -1,54 +1,29 @@ #!/usr/bin/env python +import gd_util import sys -import subprocess from Population import Population -def run_program(prog, args, stdout_file=None, space_to_tab=False): - #print "args: ", ' '.join(args) - p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE) - (stdoutdata, stderrdata) = p.communicate() - rc = p.returncode - - if stdout_file is not None: - with open(stdout_file, 'w') as ofh: - lines = stdoutdata.split('\n') - for line in lines: - line = line.strip() - if line: - if space_to_tab: - line = line.replace(' ', '\t') - print >> ofh, line - - if rc != 0: - print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args)) - print >> sys.stderr, stderrdata - sys.exit(1) - ################################################################################ -if len(sys.argv) < 7: - print >> sys.stderr, "Usage" - sys.exit(1) +if len(sys.argv) != 7: + gd_util.die('Usage') -snp_input, coverage_input, indiv_input, min_coverage, output = sys.argv[1:6] -individual_metadata = sys.argv[6:] +snp_input, coverage_input, indiv_input, min_coverage, output, ind_arg = sys.argv[1:] p_total = Population() -p_total.from_tag_list(individual_metadata) +p_total.from_wrapped_dict(ind_arg) p1 = Population() p1.from_population_file(indiv_input) if not p_total.is_superset(p1): - print >> sys.stderr, 'There is an individual in the population individuals that is not in the SNP table' - sys.exit(1) + gd_util.die('There is an individual in the population individuals that is not in the SNP table') ################################################################################ prog = 'mt_pi' args = [ prog ] - args.append(snp_input) args.append(coverage_input) args.append(min_coverage) @@ -56,5 +31,8 @@ for tag in p1.tag_list(): args.append(tag) -run_program(prog, args, stdout_file=output) +with open(output, 'w') as fh: + gd_util.run_program(prog, args, stdout=fh) + sys.exit(0) +