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1 # This is a wrapper for JAMM to use it in Galaxy
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2 # It will be accompanied with a jamm.xml file, which specifies the interface that Galaxy is showing to the user
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3 # as well as the JAMM software including JAMM.sh, the bash script that is actually called.
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4
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5 # This wrapper does the following things:
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6 # map the files (from Galaxy history) to a directory
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7 # pass the parameters from the GUI to JAMM.sh
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8 # call JAMM.sh
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9 # map the resulting tabular files back to history items
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10
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11 #import optparse
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12 import argparse, os, shutil, subprocess, sys, tempfile
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13 import shlex
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14 # importing some of the modules used, especially for symlinking, dir manipulation and tool calling.
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15 # since python2.7, argparse is preferred over optparse.
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16
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17 # for reference wrappers, see
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18 # https://bitbucket.org/fubar/rossdev/src/4a91f99b5e1953270c9b35d2ca70c325a10fcfcb/rgdev/bwa_wrapper.py?at=default
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19 # https://www.e-biogenouest.org/wiki/WrapperpythonforGalaxy:Asyntaxexample
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20
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21 def main():
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22
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23 #Read command line arguments
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24 parser = argparse.ArgumentParser()
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25 parser.add_argument('-i', dest = 'input', nargs='+') # + allows for 1 or more arguments
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26 # parser.add_argument('-c', dest = 'control', nargs='*', default=None) # allow for not supplying -c
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27 parser.add_argument('-c', dest = 'control', action='append') # allow for not supplying -c
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28 parser.add_argument('-g', dest = 'gsize')
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29 parser.add_argument('-o', dest = 'peakfile')
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30 parser.add_argument('-of', dest = 'filteredpeakfile')
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31
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32 parser.add_argument('-m', dest = 'mode')
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33 parser.add_argument('-r', dest = 'resolution')
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34 parser.add_argument('-p', dest = 'processes')
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35 parser.add_argument('-t', dest = 'type')
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36 parser.add_argument('-f', dest = 'fraglen')
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37 parser.add_argument('-b', dest = 'binsize')
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38
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39 args = parser.parse_args()
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40
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41 print "################################################"
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42 print "Wrapper debugging"
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43 print "################################################"
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44 print "Sample files:"
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45 for j in args.input:
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46 print j
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47 if args.control is not None:
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48 print "Control files:"
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49 for j in args.control:
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50 print j
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51
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52 print "output files:"
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53 print args.peakfile
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54 print args.filteredpeakfile
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55 print "current working dir:"
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56 print os.getcwd()
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57 print "dir with jammwrapper in it:"
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58 path = os.path.abspath(os.path.dirname(sys.argv[0]))
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59 print path
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60
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61 # optparse was depracted, can still be found in may of the example wrappers
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62 #parser = optparse.OptionParser()
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63 #parser.add_option( '-i', dest='input', help='input bed files' )
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64 #parser.add_option( '-c', dest='csize', help='chr sizes' )
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65 #(options, args) = parser.parse_args()
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66
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67 # create temp dir
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68 tmp_dir = tempfile.mkdtemp()
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69 os.mkdir(tmp_dir + "/sample")
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70 # symlink creation
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71 for file in args.input:
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72 filen = tmp_dir + "/sample/" + os.path.basename(os.path.splitext(file)[0])+".bed"
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73 print "input files mapped: %s" % filen
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74 os.symlink(file, filen)
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75
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76 # Here comes some unnecessary repetition
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77 # if control files are supplied, we make another tmp subdir and put those files there.
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78 # JAMM.sh is then called with one additional switch -c
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79 if args.control is not None:
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80 # symlink creation
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81 os.mkdir(tmp_dir + "/control")
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82 for file in args.control:
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83 filen = tmp_dir + "/control/" + os.path.basename(os.path.splitext(file)[0])+".bed"
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84 print "input files mapped: %s" % filen
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85 os.symlink(file, filen)
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86 command = ( "bash %s/JAMM.sh -s %s/sample -c %s/control -g %s -o results -m %s -r %s -p %s -t %s -f %s -b %s"
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87 % ( path, tmp_dir, tmp_dir, args.gsize, args.mode, args.resolution, args.processes, \
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88 args.type, args.fraglen, args.binsize ) )
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89 else:
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90 command = ( "bash %s/JAMM.sh -s %s/sample -g %s -o results -m %s -r %s -p %s -t %s -f %s -b %s"
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91 % ( path, tmp_dir, args.gsize, args.mode, args.resolution, args.processes, \
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92 args.type, args.fraglen, args.binsize ) )
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93
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94
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95 print "Command called by bash:"
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96 print command
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97 # depending on how your programm is called, it may be necessary to use shlex.split on the command string before
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98 # in this case, this was actually harmful. idk why
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99 # command = shlex.split(command)
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100 # Please read the docs for subprocess.Popen. You can't just pass as string as variables need to be extended
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101 # Note that shell = True can be a security hazard.
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102 # proc = subprocess.Popen( command, executable = '/bin/bash', shell=True )
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103 proc = subprocess.Popen( command, shell=True)
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104 returncode = proc.wait()
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105
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106 #mv files to a place where galaxy wrapper can find them
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107 # mvcommand = "mv %s/results/peaks/all.peaks.narrowPeak %s" % ( tmp_dir, args.peakfile )
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108 mvcommand = "mv results/peaks/all.peaks.narrowPeak %s" % args.peakfile
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109 os.system(mvcommand)
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110 mvcommand = "mv results/peaks/filtered.peaks.narrowPeak %s" % args.filteredpeakfile
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111 os.system(mvcommand)
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112
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113 # clean up temp dir
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114 if os.path.exists( tmp_dir ):
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115 shutil.rmtree( tmp_dir )
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116
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117 if __name__ == "__main__":
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118 main()
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119
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