Mercurial > repos > yufei-luo > s_mart

comparison SMART/bacteriaRegulatoryRegion_Detection/changeName.py @ 31:0ab839023fe4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
1 #! /usr/bin/env python
2
3 import optparse, os, sys, subprocess, tempfile, shutil
4 from optparse import OptionParser
5
6 def stop_err(msg):
7 sys.stderr.write('%s\n' % msg)
8 sys.exit()
9
10 def changeName(fileName, format, name, outputName):
11 file = open(fileName, 'r')
12 line = file.readline()
13 if format == "fasta":
14 while not line.startswith('>'):
15 line = file.readline()
16 old_name = line[1:]
17 elif format == "gff":
18 while line.startswith('#'):
19 line = file.readline()
20 old_name = (line.split('\t'))[0]
21 elif format == "sam":
22 while line.startswith('@'):
23 line = file.readline()
24 old_name = (line.split('\t'))[2]
25 file.close()
26 cmd = "sed \"s/%s/%s/g\" %s >%s " % (old_name.strip(), name.strip(), fileName, outputName)
27 proc = subprocess.Popen(cmd, shell=True)
28 proc.communicate()
29 if proc.returncode != 0:
30 raise Exception("ERROR when launching '%s'" % cmd)
31
32 def getName(fileName, format):
33 file = open(fileName, 'r')
34 line = file.readline()
35 if format == "gff":
36 while line.startswith('#'):
37 line = file.readline()
38 old_name = (line.split('\t'))[0]
39 elif format == "sam":
40 while line.startswith('@') or line.startswith('#'):
41 line = file.readline()
42 old_name = (line.split('\t'))[2]
43 file.close()
44 return old_name
45
46 def __main__():
47 #Parse Command Line
48 parser = optparse.OptionParser()
49 parser.add_option("", "--input1", dest="inputFile1", default=None, help="Choose a fasta file.")
50 parser.add_option("", "--input2", dest="inputFile2", default=None, help="Choose a gff file.")
51 parser.add_option("", "--input3", dest="inputFile3", default=None, help="Choose a sam file.")
52 parser.add_option("", "--name", dest="name", default=None, help="Change to a new name.[compulsory] if there is only one input.")
53 parser.add_option("", "--output1", dest="outputFile1", default=None, help="OutputFile1")
54 parser.add_option("", "--output2", dest="outputFile2", default=None, help="OutputFile2")
55 parser.add_option("", "--output3", dest="outputFile3", default=None, help="OutputFile3")
56 (options, args) = parser.parse_args()
57
58 #TODO:write raise Exception!!
59
60 #In case only one input
61 if options.name == None:
62 #find a default_name to unify the name for all input files
63 if options.inputFile1 != None:
64 if options.inputFile2 == None and options.inputFile3 == None:
65 raise Exception("ERROR, only one input, you should identify a new name to modify.")
66 elif options.inputFile2 != None and options.outputFile2 != None:
67 default_name = getName(options.inputFile2, 'gff')
68 changeName(options.inputFile1, 'fasta', default_name, options.outputFile1)
69 changeName(options.inputFile2, 'gff', default_name, options.outputFile2)
70 if options.inputFile3 != None and options.outputFile3 != None:
71 changeName(options.inputFile3, 'sam', default_name, options.outputFile3)
72 elif options.inputFile3 != None and options.outputFile3 != None:
73 default_name = getName(options.inputFile3, 'sam')
74 changeName(options.inputFile3, 'sam', default_name, options.outputFile3)
75 changeName(options.inputFile1, 'fasta', default_name, options.outputFile1)
76 if options.inputFile2 != None and options.outputFile2 != None:
77 changeName(options.inputFile2, 'gff', default_name, options.outputFile2)
78 else:
79 if options.inputFile1 != None and options.outputFile1 != None:
80 changeName(options.inputFile1, 'fasta', options.name, options.outputFile1)
81 if options.inputFile2 != None and options.outputFile2 != None:
82 changeName(options.inputFile2, 'gff', options.name, options.outputFile2)
83 if options.inputFile3 != None and options.outputFile3 != None:
84 changeName(options.inputFile3, 'sam', options.name, options.outputFile3)
85
86 if __name__ == '__main__':__main__()
87
88
89 #test commands:
90 #only one input:
91 #python changeName.py --input1 NC_011744.fna --name NC_test --output1 out.fna
92 #several inputs:
93 #python changeName.py --input1 NC_011744.fna --input2 NC_011744.gff --output1 out.fna --output2 out.gff
94 #python changeName.py --input1 NC_011744.fna --input2 NC_011744.gff --name NC_test --output1 out.fna --output2 out.gff
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
96 #python changeName.py --input1 NC_011744.fna --input3 out.sam --output1 out.fna --output3 out.sam
97
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