Mercurial > repos > peterjc > mira4_assembler
comparison tools/mira4/mira4_bait.py @ 0:6a88b42ce6b9 draft
Uploaded v0.0.4, previously only on the TestToolShed
| author | peterjc |
|---|---|
| date | Fri, 21 Nov 2014 06:42:56 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:6a88b42ce6b9 |
|---|---|
| 1 #!/usr/bin/env python | |
| 2 """A simple wrapper script to call MIRA4's mirabait and collect its output. | |
| 3 """ | |
| 4 import os | |
| 5 import sys | |
| 6 import subprocess | |
| 7 import shutil | |
| 8 import time | |
| 9 | |
| 10 WRAPPER_VER = "0.0.1" #Keep in sync with the XML file | |
| 11 | |
| 12 def stop_err(msg, err=1): | |
| 13 sys.stderr.write(msg+"\n") | |
| 14 sys.exit(err) | |
| 15 | |
| 16 | |
| 17 def get_version(mira_binary): | |
| 18 """Run MIRA to find its version number""" | |
| 19 # At the commend line I would use: mira -v | head -n 1 | |
| 20 # however there is some pipe error when doing that here. | |
| 21 cmd = [mira_binary, "-v"] | |
| 22 try: | |
| 23 child = subprocess.Popen(cmd, | |
| 24 stdout=subprocess.PIPE, | |
| 25 stderr=subprocess.STDOUT) | |
| 26 except Exception, err: | |
| 27 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) | |
| 28 sys.exit(1) | |
| 29 ver, tmp = child.communicate() | |
| 30 del child | |
| 31 #Workaround for -v not working in mirabait 4.0RC4 | |
| 32 if "invalid option" in ver.split("\n", 1)[0]: | |
| 33 for line in ver.split("\n", 1): | |
| 34 if " version " in line: | |
| 35 line = line.split() | |
| 36 return line[line.index("version")+1].rstrip(")") | |
| 37 stop_err("Could not determine MIRA version:\n%s" % ver) | |
| 38 return ver.split("\n", 1)[0] | |
| 39 | |
| 40 try: | |
| 41 mira_path = os.environ["MIRA4"] | |
| 42 except KeyError: | |
| 43 stop_err("Environment variable $MIRA4 not set") | |
| 44 mira_binary = os.path.join(mira_path, "mirabait") | |
| 45 if not os.path.isfile(mira_binary): | |
| 46 stop_err("Missing mirabait under $MIRA4, %r\nFolder contained: %s" | |
| 47 % (mira_binary, ", ".join(os.listdir(mira_path)))) | |
| 48 mira_ver = get_version(mira_binary) | |
| 49 if not mira_ver.strip().startswith("4.0"): | |
| 50 stop_err("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver) | |
| 51 if "-v" in sys.argv or "--version" in sys.argv: | |
| 52 print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER) | |
| 53 sys.exit(0) | |
| 54 | |
| 55 | |
| 56 format, output_choice, strand_choice, kmer_length, min_occurance, bait_file, in_file, out_file = sys.argv[1:] | |
| 57 | |
| 58 if format.startswith("fastq"): | |
| 59 format = "fastq" | |
| 60 elif format == "mira": | |
| 61 format = "maf" | |
| 62 elif format != "fasta": | |
| 63 stop_err("Was not expected format %r" % format) | |
| 64 | |
| 65 assert out_file.endswith(".dat") | |
| 66 out_file_stem = out_file[:-4] | |
| 67 | |
| 68 cmd_list = [mira_binary, "-f", format, "-t", format, | |
| 69 "-k", kmer_length, "-n", min_occurance, | |
| 70 bait_file, in_file, out_file_stem] | |
| 71 if output_choice == "pos": | |
| 72 pass | |
| 73 elif output_choice == "neg": | |
| 74 #Invert the selection... | |
| 75 cmd_list.insert(1, "-i") | |
| 76 else: | |
| 77 stop_err("Output choice should be 'pos' or 'neg', not %r" % output_choice) | |
| 78 if strand_choice == "both": | |
| 79 pass | |
| 80 elif strand_choice == "fwd": | |
| 81 #Ingore reverse strand... | |
| 82 cmd_list.insert(1, "-r") | |
| 83 else: | |
| 84 stop_err("Strand choice should be 'both' or 'fwd', not %r" % strand_choice) | |
| 85 | |
| 86 cmd = " ".join(cmd_list) | |
| 87 #print cmd | |
| 88 start_time = time.time() | |
| 89 try: | |
| 90 #Run MIRA | |
| 91 child = subprocess.Popen(cmd_list, | |
| 92 stdout=subprocess.PIPE, | |
| 93 stderr=subprocess.STDOUT) | |
| 94 except Exception, err: | |
| 95 log_manifest(manifest) | |
| 96 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) | |
| 97 sys.exit(1) | |
| 98 #Use .communicate as can get deadlocks with .wait(), | |
| 99 stdout, stderr = child.communicate() | |
| 100 assert stderr is None # Due to way we ran with subprocess | |
| 101 run_time = time.time() - start_time | |
| 102 return_code = child.returncode | |
| 103 print "mirabait took %0.2f minutes" % (run_time / 60.0) | |
| 104 | |
| 105 if return_code: | |
| 106 sys.stderr.write(stdout) | |
| 107 stop_err("Return error code %i from command:\n%s" % (return_code, cmd), | |
| 108 return_code) | |
| 109 | |
| 110 #Capture output | |
| 111 out_tmp = out_file_stem + "." + format | |
| 112 if not os.path.isfile(out_tmp): | |
| 113 sys.stderr.write(stdout) | |
| 114 stop_err("Missing output file from mirabait: %s" % out_tmp) | |
| 115 shutil.move(out_tmp, out_file) |