--- a/sampline.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,133 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Sampling random records from a file. Each record is defined by a fixed number of lines.
-
-Usage: sampline.py [options] 
-
-Options:
-  -h, --help            show this help message and exit
-  -r, --replacement     Sampling with replacement
-  -i INPUT, --input=INPUT
-                        Input file
-  -o OUTPUT, --output=OUTPUT
-                        Output file
-  -k NSAMPLE, --nSample=NSAMPLE
-                        (required) number of records to be sampled/output
-  -m RECSIZE, --recSize=RECSIZE
-                        (default=1) number of lines spanned by each record
-  -n NSKIP, --nSkip=NSKIP
-                        (default=0) number of comment lines to skip at the
-                        beginning
-
-example:
-    python sampline.py -i test10000.fastq -o out.txt --nSample=5 --recSize=4 --nSkip=0 --replacement
-"""
-
-import optparse, string, random,sys,math,itertools
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-def main():
-
-    # Parse command line    
-    parser = optparse.OptionParser( usage="%prog [options] " )
-    parser.add_option( "-r", "--replacement",  action="store_true", dest="replacement",default=False,
-                       help="Sampling with replacement" )
-    parser.add_option( "-i", "--input",  dest="input",  default=None,
-                       help="Input file" )
-    parser.add_option( "-o", "--output", dest="output", default=None,
-                       help="Output file" )
-    parser.add_option("-k","--nSample", type='int',dest="nSample",default=None,
-                      help="(required) number of records to be sampled/output" )
-    parser.add_option("-m","--recSize", type='int',dest="recSize",default=1,
-                      help="(default=1) number of lines spanned by each record" )     
-    parser.add_option("-n","--nSkip", type='int',dest="nSkip",default=0,
-                      help="(default=0) number of comment lines to skip at the beginning")    
-    options, args = parser.parse_args()
-    #assert options.region in ( 'coding', 'utr3', 'utr5', 'transcribed' ), "Invalid region argument"
-    
-    sampline(options.input,options.output,options.nSample,options.recSize,options.nSkip,options.replacement)
-
-def sample_wr(population, k):
-    "Chooses k random elements (with replacement) from a population"
-    n = len(population)
-    _random, _int = random.random, int  # speed hack
-    return [_int(_random() * n) for i in itertools.repeat(None, k)]
-
-# num of lines
-def readinput(filename):
-    try:
-        f = open (filename)
-    except:
-        print >> sys.stderr, "can't open file "+str(filename)
-        sys.exit(0)
-
-    nline = 0
-    for line in f:
-        nline = nline + 1
-    f.close()    
-    return nline
-
-def sampline(infile,outfile,nSample,recSize,nSkip,replacement):
-    # sample nSample records from file 
-    # each record contains recSize lines
-    # skip the top nSkip lines  
-    
-    nLine = readinput(infile)
-    print 'num of lines in input: ',nLine
-    print 'avoid sampling the first ',nSkip,' lines'
-    print 'lines per record: ',recSize
-
-    if (nLine-nSkip) % recSize:
-        print >> sys.stderr, "the number of lines is not dividable by record size!"
-        sys.exit(0)
-
-    nTotalRecords = (nLine-nSkip) / recSize
-    print "total number of records: ",nTotalRecords
-            
-    if replacement or nTotalRecords < nSample:
-        sel = sample_wr(range(nTotalRecords),nSample)
-    else:
-        sel = random.sample(range(nTotalRecords),nSample)
-    
-    #print len(sel), sorted(sel)
-
-    # output
-    try:
-        fout = open (outfile,'w')
-    except:
-        print >> sys.stderr, "can't open file "+str(outfile)
-        sys.exit(0)
-    fin = open(infile)
-    n = 0 # index of line
-    rec = "" # to store all content of a record
-    nrepeat = 0 # number of times a record is sampled
-    curr_rec = -1           
-    for line in fin:
-        if n < nSkip:
-            n = n + 1
-            fout.write(line)
-            continue
-        
-        if not (n-nSkip) % recSize:# a new record
-            # print the previous sampled record
-            for i in range(nrepeat):
-                fout.write(rec)
-            curr_rec = (n-nSkip)/recSize
-            nrepeat = sel.count(curr_rec)
-            if nrepeat: # sampled            
-                rec = line
-                #print curr_rec,nrepeat           
-        elif (n-nSkip)/recSize == curr_rec:
-            rec = rec + line
-        n = n + 1
-    # if the last record is selected
-    if curr_rec == nTotalRecords-1:
-        for i in range(nrepeat):
-            fout.write(rec)
-    fin.close()
-    fout.close()          
-        
-
-if __name__ == "__main__": main()