Mercurial > repos > peterjc > mira_assembler
diff mira_wrapper_v0.0.2.tar.gz/tools/sr_assembly/mira.py @ 1:e53a79816f5f
v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
author | peterjc |
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date | Thu, 16 Jun 2011 04:44:00 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mira_wrapper_v0.0.2.tar.gz/tools/sr_assembly/mira.py Thu Jun 16 04:44:00 2011 -0400 @@ -0,0 +1,107 @@ +#!/usr/bin/env python +"""A simple wrapper script to call MIRA and collect its output. +""" +import os +import sys +import subprocess +import shutil +import time + +def stop_err(msg, err=1): + sys.stderr.write(msg+"\n") + sys.exit(err) + +def tcs_to_tabular(old, new): + in_handle = open(old, "rU") + out_handle = open(new, "w") + assert in_handle.readline() == "#TCS V1.0\n" + assert in_handle.readline() == "#\n" + assert in_handle.readline() == "# contig name padPos upadPos | B Q | tcov covA covC covG covT cov* | qA qC qG qT q* | S | Tags\n" + assert in_handle.readline() == "#\n" + out_handle.write("#%s\n" % "\t".join(["contig", "pasPos", "upadPos", "B", "Q", + "tcov", "covA", "covC", "covG", "covT", "cov*", + "qA", "qC", "qG", "qT", "q*", "S", "Tags"])) + for line in in_handle: + parts = line.rstrip("\n").split(None,22) + assert parts[3] == parts[6] == parts[13] == parts[19] == parts[21] == "|" + wanted = parts[:3] + parts[4:6]+parts[7:13]+parts[14:19]+parts[20:21]+parts[22:] + out_handle.write("%s\n" % "\t".join(wanted)) + out_handle.close() + in_handle.close() + +def collect_output(temp, name): + n3 = (temp, name, name, name) + f = "%s/%s_assembly/%s_d_results" % (temp, name, name) + if not os.path.isdir(f): + stop_err("Missing output folder") + if not os.listdir(f): + stop_err("Empty output folder") + for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta), + ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual), + ("%s/%s_out.wig" % (f, name), out_wig), + ("%s/%s_out.caf" % (f, name), out_caf), + ("%s/%s_out.ace" % (f, name), out_ace)]: + if not os.path.isfile(old): + stop_err("Missing %s output file" % os.path.splitext(old)[-1]) + else: + shutil.move(old, new) + tcs_to_tabular("%s/%s_assembly/%s_d_results/%s_out.tcs" % n3, out_tcs) + +def clean_up(temp, name): + folder = "%s/%s_assembly" % (temp, name) + if os.path.isdir(folder): + shutil.rmtree(folder) + +#TODO - Run MIRA in /tmp or a configurable directory? +#Currently Galaxy puts us somewhere safe like: +#/opt/galaxy-dist/database/job_working_directory/846/ +temp = "." +name, out_fasta, out_qual, out_tcs, out_ace, out_caf, out_wig, out_log = sys.argv[1:9] + +start_time = time.time() +cmd = " ".join(sys.argv[9:]) + +assert os.path.isdir(temp) +d = "%s_assembly" % name +assert not os.path.isdir(d) +try: + #Check path access + os.mkdir(d) +except Exception, err: + sys.stderr.write("Error making directory %s\n%s" % (d, err)) + sys.exit(1) + +#print os.path.abspath(".") +#print cmd + +handle = open(out_log, "w") +try: + #Run MIRA + child = subprocess.Popen(sys.argv[9:], + stdout=handle, + stderr=subprocess.STDOUT) +except Exception, err: + sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) + #TODO - call clean up? + handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) + handle.close() + sys.exit(1) +#Use .communicate as can get deadlocks with .wait(), +stdout, stderr = child.communicate() +assert not stdout and not stderr #Should be empty as sent to handle +run_time = time.time() - start_time +return_code = child.returncode +handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0)) +print "MIRA took %0.2f minutes" % (run_time / 60.0) +if return_code: + handle.write("Return error code %i from command:\n" % return_code) + handle.write(cmd + "\n") + handle.close() + clean_up(temp, name) + stop_err("Return error code %i from command:\n%s" % (return_code, cmd), + return_code) +handle.close() + +collect_output(temp, name) +clean_up(temp, name) +print "Done"