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1 #! /usr/bin/env python
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2
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3 import optparse, os, sys, subprocess, tempfile, shutil
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4 from optparse import OptionParser
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5
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6 def stop_err(msg):
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7 sys.stderr.write('%s\n' % msg)
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8 sys.exit()
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9
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10 def changeName(fileName, format, name, outputName):
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11 file = open(fileName, 'r')
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12 line = file.readline()
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13 if format == "fasta":
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14 while not line.startswith('>'):
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15 line = file.readline()
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16 old_name = line[1:]
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17 elif format == "gff":
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18 while line.startswith('#'):
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19 line = file.readline()
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20 old_name = (line.split('\t'))[0]
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21 elif format == "sam":
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22 while line.startswith('@'):
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23 line = file.readline()
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24 old_name = (line.split('\t'))[2]
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25 file.close()
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26 cmd = "sed \"s/%s/%s/g\" %s >%s " % (old_name.strip(), name.strip(), fileName, outputName)
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27 proc = subprocess.Popen(cmd, shell=True)
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28 proc.communicate()
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29 if proc.returncode != 0:
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30 raise Exception("ERROR when launching '%s'" % cmd)
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31
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32 def getName(fileName, format):
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33 file = open(fileName, 'r')
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34 line = file.readline()
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35 if format == "gff":
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36 while line.startswith('#'):
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37 line = file.readline()
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38 old_name = (line.split('\t'))[0]
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39 elif format == "sam":
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40 while line.startswith('@') or line.startswith('#'):
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41 line = file.readline()
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42 old_name = (line.split('\t'))[2]
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43 file.close()
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44 return old_name
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45
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46 def __main__():
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47 #Parse Command Line
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48 parser = optparse.OptionParser()
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49 parser.add_option("", "--input1", dest="inputFile1", default=None, help="Choose a fasta file.")
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50 parser.add_option("", "--input2", dest="inputFile2", default=None, help="Choose a gff file.")
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51 parser.add_option("", "--input3", dest="inputFile3", default=None, help="Choose a sam file.")
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52 parser.add_option("", "--name", dest="name", default=None, help="Change to a new name.[compulsory] if there is only one input.")
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53 parser.add_option("", "--output1", dest="outputFile1", default=None, help="OutputFile1")
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54 parser.add_option("", "--output2", dest="outputFile2", default=None, help="OutputFile2")
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55 parser.add_option("", "--output3", dest="outputFile3", default=None, help="OutputFile3")
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56 (options, args) = parser.parse_args()
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57
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58 #TODO:write raise Exception!!
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59
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60 #In case only one input
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61 if options.name == None:
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62 #find a default_name to unify the name for all input files
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63 if options.inputFile1 != None:
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64 if options.inputFile2 == None and options.inputFile3 == None:
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65 raise Exception("ERROR, only one input, you should identify a new name to modify.")
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66 elif options.inputFile2 != None and options.outputFile2 != None:
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67 default_name = getName(options.inputFile2, 'gff')
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68 changeName(options.inputFile1, 'fasta', default_name, options.outputFile1)
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69 changeName(options.inputFile2, 'gff', default_name, options.outputFile2)
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70 if options.inputFile3 != None and options.outputFile3 != None:
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71 changeName(options.inputFile3, 'sam', default_name, options.outputFile3)
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72 elif options.inputFile3 != None and options.outputFile3 != None:
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73 default_name = getName(options.inputFile3, 'sam')
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74 changeName(options.inputFile3, 'sam', default_name, options.outputFile3)
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75 changeName(options.inputFile1, 'fasta', default_name, options.outputFile1)
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76 if options.inputFile2 != None and options.outputFile2 != None:
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77 changeName(options.inputFile2, 'gff', default_name, options.outputFile2)
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78 else:
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79 if options.inputFile1 != None and options.outputFile1 != None:
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80 changeName(options.inputFile1, 'fasta', options.name, options.outputFile1)
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81 if options.inputFile2 != None and options.outputFile2 != None:
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82 changeName(options.inputFile2, 'gff', options.name, options.outputFile2)
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83 if options.inputFile3 != None and options.outputFile3 != None:
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84 changeName(options.inputFile3, 'sam', options.name, options.outputFile3)
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85
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86 if __name__ == '__main__':__main__()
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87
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88
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89 #test commands:
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90 #only one input:
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91 #python changeName.py --input1 NC_011744.fna --name NC_test --output1 out.fna
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92 #several inputs:
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93 #python changeName.py --input1 NC_011744.fna --input2 NC_011744.gff --output1 out.fna --output2 out.gff
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94 #python changeName.py --input1 NC_011744.fna --input2 NC_011744.gff --name NC_test --output1 out.fna --output2 out.gff
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95 #python changeName.py --input1 NC_011744.fna --input2 NC_011744.gff --input3 NC_011744.sam --name NC_test2 --output1 out.fna --output2 out.gff --output3 out.sam
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96 #python changeName.py --input1 NC_011744.fna --input3 out.sam --output1 out.fna --output3 out.sam
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97
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98
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99 |
