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comparison sampline.py @ 11:b7f1d9f8f3bc

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author xuebing
date Sat, 10 Mar 2012 07:59:27 -0500
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10:1558594a3c2e 11:b7f1d9f8f3bc
1 #!/usr/bin/env python
2
3 """
4 Sampling random records from a file. Each record is defined by a fixed number of lines.
5
6 Usage: sampline.py [options]
7
8 Options:
9 -h, --help show this help message and exit
10 -r, --replacement Sampling with replacement
11 -i INPUT, --input=INPUT
12 Input file
13 -o OUTPUT, --output=OUTPUT
14 Output file
15 -k NSAMPLE, --nSample=NSAMPLE
16 (required) number of records to be sampled/output
17 -m RECSIZE, --recSize=RECSIZE
18 (default=1) number of lines spanned by each record
19 -n NSKIP, --nSkip=NSKIP
20 (default=0) number of comment lines to skip at the
21 beginning
22
23 example:
24 python sampline.py -i test10000.fastq -o out.txt --nSample=5 --recSize=4 --nSkip=0 --replacement
25 """
26
27 import optparse, string, random,sys,math,itertools
28
29 assert sys.version_info[:2] >= ( 2, 4 )
30
31 def main():
32
33 # Parse command line
34 parser = optparse.OptionParser( usage="%prog [options] " )
35 parser.add_option( "-r", "--replacement", action="store_true", dest="replacement",default=False,
36 help="Sampling with replacement" )
37 parser.add_option( "-i", "--input", dest="input", default=None,
38 help="Input file" )
39 parser.add_option( "-o", "--output", dest="output", default=None,
40 help="Output file" )
41 parser.add_option("-k","--nSample", type='int',dest="nSample",default=None,
42 help="(required) number of records to be sampled/output" )
43 parser.add_option("-m","--recSize", type='int',dest="recSize",default=1,
44 help="(default=1) number of lines spanned by each record" )
45 parser.add_option("-n","--nSkip", type='int',dest="nSkip",default=0,
46 help="(default=0) number of comment lines to skip at the beginning")
47 options, args = parser.parse_args()
48 #assert options.region in ( 'coding', 'utr3', 'utr5', 'transcribed' ), "Invalid region argument"
49
50 sampline(options.input,options.output,options.nSample,options.recSize,options.nSkip,options.replacement)
51
52 def sample_wr(population, k):
53 "Chooses k random elements (with replacement) from a population"
54 n = len(population)
55 _random, _int = random.random, int # speed hack
56 return [_int(_random() * n) for i in itertools.repeat(None, k)]
57
58 # num of lines
59 def readinput(filename):
60 try:
61 f = open (filename)
62 except:
63 print >> sys.stderr, "can't open file "+str(filename)
64 sys.exit(0)
65
66 nline = 0
67 for line in f:
68 nline = nline + 1
69 f.close()
70 return nline
71
72 def sampline(infile,outfile,nSample,recSize,nSkip,replacement):
73 # sample nSample records from file
74 # each record contains recSize lines
75 # skip the top nSkip lines
76
77 nLine = readinput(infile)
78 print 'num of lines in input: ',nLine
79 print 'avoid sampling the first ',nSkip,' lines'
80 print 'lines per record: ',recSize
81
82 if (nLine-nSkip) % recSize:
83 print >> sys.stderr, "the number of lines is not dividable by record size!"
84 sys.exit(0)
85
86 nTotalRecords = (nLine-nSkip) / recSize
87 print "total number of records: ",nTotalRecords
88
89 if replacement or nTotalRecords < nSample:
90 sel = sample_wr(range(nTotalRecords),nSample)
91 else:
92 sel = random.sample(range(nTotalRecords),nSample)
93
94 #print len(sel), sorted(sel)
95
96 # output
97 try:
98 fout = open (outfile,'w')
99 except:
100 print >> sys.stderr, "can't open file "+str(outfile)
101 sys.exit(0)
102 fin = open(infile)
103 n = 0 # index of line
104 rec = "" # to store all content of a record
105 nrepeat = 0 # number of times a record is sampled
106 curr_rec = -1
107 for line in fin:
108 if n < nSkip:
109 n = n + 1
110 fout.write(line)
111 continue
112
113 if not (n-nSkip) % recSize:# a new record
114 # print the previous sampled record
115 for i in range(nrepeat):
116 fout.write(rec)
117 curr_rec = (n-nSkip)/recSize
118 nrepeat = sel.count(curr_rec)
119 if nrepeat: # sampled
120 rec = line
121 #print curr_rec,nrepeat
122 elif (n-nSkip)/recSize == curr_rec:
123 rec = rec + line
124 n = n + 1
125 # if the last record is selected
126 if curr_rec == nTotalRecords-1:
127 for i in range(nrepeat):
128 fout.write(rec)
129 fin.close()
130 fout.close()
131
132
133 if __name__ == "__main__": main()