Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/dbSplit.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 #!/usr/bin/env python
2
3
4 ##@file
5 # Split the input fasta file in several output files
6 # usage: dbSplit.py [ options ]
7 # options:
8 # -h: this help
9 # -i: name of the input file (format='fasta')
10 # -n: number of sequences per output file (default=1)
11 # -d: record the output fasta files in a directory called 'batches'
12 # -s: use the sequence header if '-n 1' (otherwise 'batch_00X')"
13 # -p: use a prefix for the output files (default='batch')"
14 # -v: verbose (default=0/1)
15
16
17 import sys
18 import getopt
19
20 from commons.core.seq.FastaUtils import FastaUtils
21
22
23 ## Give the list of the command-line options
24 #
25 def help():
26 print
27 print "usage: dbSplit.py [ options ]"
28 print "options:"
29 print " -h: this help"
30 print " -i: name of the input file (format='fasta')"
31 print " -n: number of sequences per batch file (default=1)"
32 print " -d: record the output fasta files in a directory called 'batches'"
33 print " -s: use the sequence header if '-n 1' (otherwise 'batch_00X')"
34 print " -p: use a prefix for the output files (default='batch')"
35 print " -v: verbosity level (default=0/1/2)"
36 print
37
38
39 ## Split the input fasta file in several output files
40 #
41 def main():
42 inFile = ""
43 nbSeqPerBatch = 1
44 newDir = False
45 useSeqHeader = False
46 prefix = "batch"
47 verbose = 0
48
49 try:
50 opts, args = getopt.getopt( sys.argv[1:], "hi:n:dsp:v:" )
51 except getopt.GetoptError, err:
52 sys.stderr.write( "%s\n" % ( str(err) ) )
53 help()
54 sys.exit(1)
55 for o,a in opts:
56 if o == "-h":
57 help()
58 sys.exit(0)
59 elif o == "-i":
60 inFile = a
61 elif o == "-n":
62 nbSeqPerBatch = int(a)
63 elif o == "-d":
64 newDir = True
65 elif o == "-s":
66 useSeqHeader = True
67 elif o == "-p":
68 prefix = a
69 elif o == "-v":
70 verbose = int(a)
71
72 if inFile == "":
73 msg = "ERROR: missing input file (-i)"
74 sys.stderr.write( "%s\n" % ( msg ) )
75 help()
76 sys.exit(1)
77
78 if verbose > 0:
79 print "START %s" % ( sys.argv[0].split("/")[-1] )
80 sys.stdout.flush()
81
82 FastaUtils.dbSplit( inFile, nbSeqPerBatch, newDir, useSeqHeader, prefix, verbose )
83
84 if verbose > 0:
85 print "END %s" % ( sys.argv[0].split("/")[-1] )
86 sys.stdout.flush()
87
88 return 0
89
90
91 if __name__ == "__main__":
92 main()