Mercurial > repos > peterjc > mira_assembler

annotate tools/sr_assembly/mira.py @ 5:216bf640baaf draft

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Uploaded v0.0.4 which fixes a problem in v0.0.3 with the backbone arguments.
author peterjc
date Wed, 09 May 2012 12:40:06 -0400
parents 117cce3296af
children 3e7eca1f5d04
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1 #!/usr/bin/env python
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2 """A simple wrapper script to call MIRA and collect its output.
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3 """
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4 import os
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5 import sys
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6 import subprocess
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7 import shutil
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8 import time
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9
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10 def stop_err(msg, err=1):
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11 sys.stderr.write(msg+"\n")
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12 sys.exit(err)
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13
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14 def collect_output(temp, name):
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15 n3 = (temp, name, name, name)
3
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16 f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
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17 if not os.path.isdir(f):
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18 stop_err("Missing output folder")
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19 if not os.listdir(f):
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20 stop_err("Empty output folder")
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21 missing = []
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22 for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
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23 ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
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24 ("%s/%s_out.wig" % (f, name), out_wig),
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25 ("%s/%s_out.caf" % (f, name), out_caf),
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26 ("%s/%s_out.ace" % (f, name), out_ace)]:
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27 if not os.path.isfile(old):
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28 missing.append(os.path.splitext(old)[-1])
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29 else:
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30 shutil.move(old, new)
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31 if missing:
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32 stop_err("Missing output files: %s" % ", ".join(missing))
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33
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34 def clean_up(temp, name):
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35 folder = "%s/%s_assembly" % (temp, name)
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36 if os.path.isdir(folder):
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37 shutil.rmtree(folder)
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38
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39 #TODO - Run MIRA in /tmp or a configurable directory?
3
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40 #Currently Galaxy puts us somewhere safe like:
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41 #/opt/galaxy-dist/database/job_working_directory/846/
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42 temp = "."
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43 name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
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44
0
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45 start_time = time.time()
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46 cmd_list =sys.argv[8:]
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47 cmd = " ".join(cmd_list)
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48
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49 assert os.path.isdir(temp)
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50 d = "%s_assembly" % name
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51 assert not os.path.isdir(d), "Path %s already exists" % d
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52 try:
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53 #Check path access
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54 os.mkdir(d)
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55 except Exception, err:
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56 sys.stderr.write("Error making directory %s\n%s" % (d, err))
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57 sys.exit(1)
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58
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59 #print os.path.abspath(".")
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60 #print cmd
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61
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62 handle = open(out_log, "w")
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63 try:
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64 #Run MIRA
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65 child = subprocess.Popen(cmd_list,
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66 stdout=handle,
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67 stderr=subprocess.STDOUT)
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68 except Exception, err:
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69 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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70 #TODO - call clean up?
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71 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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72 handle.close()
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73 sys.exit(1)
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74 #Use .communicate as can get deadlocks with .wait(),
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75 stdout, stderr = child.communicate()
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76 assert not stdout and not stderr #Should be empty as sent to handle
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77 run_time = time.time() - start_time
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78 return_code = child.returncode
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79 handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
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80 print "MIRA took %0.2f minutes" % (run_time / 60.0)
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81 if return_code:
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82 handle.write("Return error code %i from command:\n" % return_code)
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83 handle.write(cmd + "\n")
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84 handle.close()
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85 clean_up(temp, name)
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86 stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
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87 return_code)
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88 handle.close()
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89
4
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90 #print "Collecting output..."
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91 collect_output(temp, name)
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92
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93 #print "Cleaning up..."
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94 clean_up(temp, name)
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95
0
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96 print "Done"