changeset 1:fc8ab6f2276a default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sampline.py	Thu Sep 08 22:30:00 2011 -0400
@@ -0,0 +1,133 @@
+#!/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()