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1 #!/usr/bin/env python
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2 import optparse
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3 import os
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4 import sys
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5 import tempfile
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6 import subprocess
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7 import shutil
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8 import logging
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9
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10 assert sys.version_info[:2] >= ( 2, 6 )
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11
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12 log = logging.getLogger(__name__)
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13 working_directory = os.getcwd()
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14 tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stderr').name
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15 tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stdout').name
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16
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17
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18 def stop_err( msg ):
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19 sys.stderr.write( "%s\n" % msg )
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20 sys.exit()
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21
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22
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23 def read_stderr():
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24 stderr = ''
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25 if(os.path.exists(tmp_stderr_name)):
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26 with open(tmp_stderr_name, 'rb') as tmp_stderr:
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27 buffsize = 1048576
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28 try:
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29 while True:
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30 stderr += tmp_stderr.read(buffsize)
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31 if not stderr or len(stderr) % buffsize != 0:
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32 break
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33 except OverflowError:
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34 pass
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35 return stderr
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36
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37
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38 def execute(command, stdin=None):
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39 with open(tmp_stderr_name, 'wb') as tmp_stderr:
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40 with open(tmp_stdout_name, 'wb') as tmp_stdout:
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41 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
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42 returncode = proc.wait()
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43 if returncode != 0:
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44 raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
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45
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46
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47 def delete_file(path):
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48 if os.path.exists(path):
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49 try:
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50 os.remove(path)
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51 except:
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52 pass
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53
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54
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55 def delete_directory(directory):
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56 if os.path.exists(directory):
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57 try:
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58 shutil.rmtree(directory)
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59 except:
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60 pass
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61
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62
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63 def symlink(source, link_name):
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64 import platform
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65 if platform.system() == 'Windows':
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66 import win32file
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67 win32file.CreateSymbolicLink(source, link_name, 1)
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68 else:
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69 os.symlink(source, link_name)
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70
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71
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72 def copy_to_working_directory(data_file, relative_path):
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73 if os.path.abspath(data_file) != os.path.abspath(relative_path):
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74 shutil.copy(data_file, relative_path)
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75 return relative_path
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76
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77
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78 def __main__():
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79 run_script()
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80
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81 #ENDTEMPLATE
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82
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83
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84 def run_script():
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85 parser = optparse.OptionParser()
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86 parser.add_option("--input")
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87 parser.add_option("--export_spreadsheet", action="store_true", dest="export_spreadsheet")
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88 parser.add_option("--append_unmodified_peptide", action="store_true", dest="append_unmodified_peptide", default=False)
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89 parser.set_defaults(export_spreadsheet=False)
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90 (options, args) = parser.parse_args()
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91
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92 copy_to_working_directory(options.input, "input.pep.xml")
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93 # Trans-Proteomic Pipeline - cgi-bin/PepXMLViewer.cgi
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94 cmd = "PepXMLViewer.cgi -I input.pep.xml"
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95 cmd = "%s %s" % (cmd, "-B exportSpreadsheet")
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96 if options.export_spreadsheet:
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97 cmd = "%s %s" % (cmd, "1")
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98 else:
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99 cmd = "%s %s" % (cmd, "0")
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100 execute(cmd)
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101 if options.append_unmodified_peptide:
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102 from csv import reader
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103 csv_opts = {'delimiter': '\t'}
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104 first = True
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105 with open("tmp.xls", "w") as output:
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106 peptide_index = None
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107 for row in reader(open("input.pep.xls", "r"), **csv_opts):
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108 if first:
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109 peptide_index = row.index("peptide")
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110 row.append("unmodified_peptide")
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111 output.write("\t".join(row))
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112 output.write("\n")
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113 first = False
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114 else:
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115 row.append(unmodify(row[peptide_index]))
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116 output.write("\t".join(row))
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117 output.write("\n")
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118 execute("mv tmp.xls input.pep.xls")
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119
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120
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121 def unmodify(peptide):
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122 """
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123
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124 >>> from re import sub
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125 >>> sub(r'\[(\-|\d|\.)+\]', '', 'A[-12.34]B')
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126 'AB'
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127 """
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128 from re import sub
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129 peptide = sub(r'\[(\-|\d|\.)+\]', '', peptide)
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130 peptide = sub(r'^.\.|\..$|n|c', '', peptide)
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131 #peptide = sub(r'\..$', '', peptide)
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132 #peptide = sub(r'\[.+\]', '', peptide)
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133 return peptide
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134
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135
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136 if __name__ == '__main__':
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137 __main__()
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