Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/dbBestLength.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 ## @file
4 # This program extracts the n longest sequences from the input fasta file.
5 # usage: dbBestLength.py [ options ]
6 # options:
7 # -h: this help
8 # -i: name of the input fasta file
9 # -n: maximum number of sequences in the output file (default=20)
10 # -o: name of the output fasta file (default=inFileName+'.best20')
11 # -v: verbose (default=0/1/2)
12
13 import os
14 import sys
15 import getopt
16
17 if not os.environ.has_key( "REPET_PATH" ):
18 print "*** Error: no environment variable REPET_PATH"
19 sys.exit(1)
20 sys.path.append( os.environ["REPET_PATH"] )
21
22 from pyRepet.seq.fastaDB import *
23
24
25 def help():
26 """
27 Give the list of the command-line options.
28 """
29 print
30 print "usage: dbBestLength.py [ options ]"
31 print "options:"
32 print " -h: this help"
33 print " -i: name of the input fasta file"
34 print " -n: maximum number of sequences in the output file (default=20)"
35 print " -o: name of the output fasta file (default=inFileName+'.best20')"
36 print " -v: verbose (default=0/1/2)"
37 print
38
39
40 def main():
41 """
42 This program extracts the n longest sequences from the input fasta file.
43 """
44
45 inFileName = ""
46 nbSeq = 20
47 outFileName = ""
48 verbose = 0
49
50 try:
51 opts, args = getopt.getopt(sys.argv[1:],"hi:n:o:v:")
52 except getopt.GetoptError, err:
53 print str(err)
54 help()
55 sys.exit(1)
56 for o,a in opts:
57 if o == "-h":
58 help()
59 sys.exit(0)
60 elif o == "-i":
61 inFileName = a
62 elif o == "-n":
63 nbSeq = a
64 elif o == "-o":
65 outFileName = a
66 elif o == "-v":
67 verbose = int(a)
68
69 if inFileName == "":
70 print "ERROR: missing input file (-i)"
71 help()
72 sys.exit(1)
73
74 if verbose > 0:
75 print "START dbBestLength.py"
76 sys.stdout.flush()
77
78 if outFileName == "":
79 outFileName = "%s.best%s" % ( inFileName, nbSeq )
80
81 log = dbBestLength( nbSeq, inFileName, outFileName, verbose )
82 if log != 0:
83 print "ERROR: dbBestLength() returned %i" % ( log )
84 sys.exit(1)
85
86 if verbose > 0:
87 print "END dbBestLength.py"
88 sys.stdout.flush()
89
90 return 0
91
92
93 if __name__ == "__main__":
94 main()