Mercurial > repos > peterjc > mira_assembler

annotate tools/sr_assembly/mira.py @ 0:03b240624b5a

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 16:23:51 -0400
parents
children 298f5c1d9521
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
1 #!/usr/bin/env python
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
2 """A simple wrapper script to call MIRA and collect its output.
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
3 """
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
4 import os
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
5 import sys
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
6 import subprocess
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
7 import shutil
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
8 import time
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
9
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
10 def stop_err(msg, err=1):
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
11 sys.stderr.write(msg+"\n")
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
12 sys.exit(err)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
13
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
14 def tcs_to_tabular(old, new):
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
15 in_handle = open(old, "rU")
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
16 out_handle = open(new, "w")
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
17 assert in_handle.readline() == "#TCS V1.0\n"
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
18 assert in_handle.readline() == "#\n"
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
19 assert in_handle.readline() == "# contig name padPos upadPos | B Q | tcov covA covC covG covT cov* | qA qC qG qT q* | S | Tags\n"
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
20 assert in_handle.readline() == "#\n"
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
21 out_handle.write("#%s\n" % "\t".join(["contig", "pasPos", "upadPos", "B", "Q",
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
22 "tcov", "covA", "covC", "covG", "covT", "cov*",
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
23 "qA", "qC", "qG", "qT", "q*", "S", "Tags"]))
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
24 for line in in_handle:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
25 parts = line.rstrip("\n").split(None,22)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
26 assert parts[3] == parts[6] == parts[13] == parts[19] == parts[21] == "|"
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
27 wanted = parts[:3] + parts[4:6]+parts[7:13]+parts[14:19]+parts[20:21]+parts[22:]
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
28 out_handle.write("%s\n" % "\t".join(wanted))
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
29 out_handle.close()
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
30 in_handle.close()
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
31
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
32 def collect_output(temp, name):
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
33 n3 = (temp, name, name, name)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
34 tcs_to_tabular("%s/%s_assembly/%s_d_results/%s_out.tcs" % n3, out_tcs)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
35 for old, new in [("%s/%s_assembly/%s_d_results/%s_out.unpadded.fasta" % n3, out_fasta),
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
36 ("%s/%s_assembly/%s_d_results/%s_out.unpadded.fasta.qual" % n3, out_qual),
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
37 ("%s/%s_assembly/%s_d_results/%s_out.wig" % n3, out_wig),
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
38 ("%s/%s_assembly/%s_d_results/%s_out.caf" % n3, out_caf),
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
39 ("%s/%s_assembly/%s_d_results/%s_out.ace" % n3, out_ace)]:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
40 if not os.path.isfile(old):
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
41 stop_err("Missing %s output file" % os.path.splitext(old)[-1])
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
42 else:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
43 shutil.move(old, new)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
44
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
45 def clean_up(temp, name):
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
46 folder = "%s/%s_assembly" % (temp, name)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
47 if os.path.isdir(folder):
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
48 shutil.rmtree(folder)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
49
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
50 #TODO - Run MIRA in /tmp or a configurable directory?
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
51 temp = "."
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
52 name, out_fasta, out_qual, out_tcs, out_ace, out_caf, out_wig, out_log = sys.argv[1:9]
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
53 start_time = time.time()
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
54 try:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
55 cmd = " ".join(sys.argv[9:])
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
56 child = subprocess.Popen(sys.argv[9:],
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
57 stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
58 except Exception, err:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
59 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
60 sys.exit(1)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
61 #Use .communicate as can get deadlocks with .wait(),
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
62 stdout, stderr = child.communicate()
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
63 run_time = time.time() - start_time
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
64 return_code = child.returncode
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
65 handle = open(out_log, "w")
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
66 handle.write(stdout)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
67 handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
68 print "MIRA took %0.2f minutes" % (run_time / 60.0)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
69 if return_code:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
70 handle.write("Return error code %i from command:\n" % return_code)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
71 handle.write(cmd + "\n")
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
72 handle.close()
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
73 clean_up(temp, name)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
74 stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
75 return_code)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
76 handle.close()
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
77
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
78 collect_output(temp, name)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
79 clean_up(temp, name)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
80 print "Done"