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1 #!/usr/bin/env python
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2
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3 import subprocess
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4 import tempfile
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5 import sys
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6 import os
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7 import re
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8 from optparse import OptionParser
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9
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10
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11 class MdustWrapper(object):
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12
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13 def __init__(self):
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14 self._options = None
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15
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16 def stop_err(self, msg):
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17 sys.stderr.write("%s\n" % msg)
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18 sys.exit()
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19
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20 def setAttributesFromCmdLine(self):
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21 description = "mdust_wrapper"
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22 description += "\nWrapper for mdust\n"
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23 description += "example: mdust_wrapper.py -i seq.fasta -v 27\n"
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24 parser = OptionParser(description = description, version = "0.1")
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25 parser.add_option("-i", "--input", dest = "FastaFile", action = "store", type = "string", help = "Input Fasta File name [compulsory] [format: Fasta]", default = "")
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26 parser.add_option("-o", "--output", dest = "outFile", action = "store", type = "string", help = "output File name [compulsory] [format: fasta,tab or bed]", default = "")
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27 parser.add_option("-v", "--cutoff", dest = "cutoff", action = "store", type = "int", help = "cutoff", default = 28)
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28 parser.add_option("-w", "--wsize", dest = "wsize", action = "store", type = "int", help = "window size", default = 3)
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29 parser.add_option("-m", "--maskingletter", dest = "maskingletter", action = "store", type = "string", help = "masking letter", default = "N")
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30 parser.add_option("-f", "--format", dest = "format", action = "store", type = "string", help = "format", default = "default")
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31 options = parser.parse_args()[0]
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32 self._setAttributesFromOptions(options)
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33
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34
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35 def _setAttributesFromOptions(self, options):
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36 self._options = options
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37
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38 if self._options.FastaFile == "":
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39 raise Exception("Missing input file, please provide fasta file with -i file !")
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40 if self._options.outFile == "":
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41 raise Exception("Missing output file, please provide output file with -o file !")
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42
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43
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44 def run(self):
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45
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46 prg = "mdust"
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47 args = ""
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48 args += " %s" % self._options.FastaFile
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49 args += " -v %d" % self._options.cutoff
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50 args += " -w %d" % self._options.wsize
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51 args += " -m %s" % self._options.maskingletter
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52 if self._options.format == "tab" or self._options.format == "bed":
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53 args += " -c "
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54 cmd = "%s %s" %(prg, args)
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55
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56 try:
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57 tmp_err = tempfile.NamedTemporaryFile().name
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58 tmp_out = "outfile"
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59 tmp_stderr = open( tmp_err, 'wb' )
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60 tmp_stdout = open( tmp_out, 'wb' )
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61 proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )
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62 returncode = proc.wait()
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63 tmp_stderr.close()
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64 # get stderr, allowing for case where it's very large
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65 tmp_stderr = open( tmp_err, 'rb' )
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66 tmp_stdout = open( tmp_out, 'rb' )
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67
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68 stderr = ''
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69 stdout = ''
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70 buffsize = 1048576
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71 try:
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72 while True:
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73 stdout += tmp_stdout.read( buffsize )
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74 if not stdout or len( stdout ) % buffsize != 0:
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75 break
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76 except OverflowError:
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77 pass
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78 tmp_stdout.close()
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79
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80 try:
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81 while True:
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82 stderr += tmp_stderr.read( buffsize )
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83 if not stderr or len( stderr ) % buffsize != 0:
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84 break
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85 except OverflowError:
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86 pass
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87 tmp_stderr.close()
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88 if stderr:
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89 raise Exception, stderr
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90 except Exception, e:
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91 self.stop_err( 'Error with mdust :\n' + str( e ) )
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92
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93 if self._options.format == 'bed':
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94 with open(tmp_out,"r") as fin:
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95 with open(self._options.outFile, "w") as fout:
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96 lineNumber = 0
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97 for line in fin:
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98 lineNumber += 1
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99 m = re.search(r"^(\S+)\t(\d+)\t(\d+)\t(\d+)$", line)
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100 if m is not None:
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101 fout.write("%s\t%d\t%d\n" % (m.group(1), int(m.group(3))-1, int(m.group(4))))
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102 if m is None:
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103 raise Exception("\nLine %d '%s' does not has a mdust format." % (lineNumber, line))
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104 else:
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105 os.rename(tmp_out,self._options.outFile)
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106
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107
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108
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109
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110 if __name__ == "__main__":
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111 iWrapper = MdustWrapper()
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112 iWrapper.setAttributesFromCmdLine()
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113 iWrapper.run()
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