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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/dbSplit.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+
+
+##@file
+# Split the input fasta file in several output files
+# usage: dbSplit.py [ options ]
+# options:
+#      -h: this help
+#      -i: name of the input file (format='fasta')
+#      -n: number of sequences per output file (default=1)
+#      -d: record the output fasta files in a directory called 'batches'
+#      -s: use the sequence header if '-n 1' (otherwise 'batch_00X')"
+#      -p: use a prefix for the output files (default='batch')"
+#      -v: verbose (default=0/1)
+
+
+import sys
+import getopt
+
+from commons.core.seq.FastaUtils import FastaUtils
+
+
+## Give the list of the command-line options
+#
+def help():
+    print
+    print "usage: dbSplit.py [ options ]"
+    print "options:"
+    print "     -h: this help"
+    print "     -i: name of the input file (format='fasta')"
+    print "     -n: number of sequences per batch file (default=1)"
+    print "     -d: record the output fasta files in a directory called 'batches'"
+    print "     -s: use the sequence header if '-n 1' (otherwise 'batch_00X')"
+    print "     -p: use a prefix for the output files (default='batch')"
+    print "     -v: verbosity level (default=0/1/2)"
+    print
+
+
+## Split the input fasta file in several output files
+#
+def main():
+    inFile = ""
+    nbSeqPerBatch = 1
+    newDir = False
+    useSeqHeader = False
+    prefix = "batch"
+    verbose = 0
+
+    try:
+        opts, args = getopt.getopt( sys.argv[1:], "hi:n:dsp:v:" )
+    except getopt.GetoptError, err:
+        sys.stderr.write( "%s\n" % ( str(err) ) )
+        help()
+        sys.exit(1)
+    for o,a in opts:
+        if o == "-h":
+            help()
+            sys.exit(0)
+        elif o == "-i":
+            inFile = a
+        elif o == "-n":
+            nbSeqPerBatch = int(a)
+        elif o == "-d":
+            newDir = True
+        elif o == "-s":
+            useSeqHeader = True
+        elif o == "-p":
+            prefix = a
+        elif o == "-v":
+            verbose = int(a)
+
+    if inFile == "":
+        msg = "ERROR: missing input file (-i)"
+        sys.stderr.write( "%s\n" % ( msg ) )
+        help()
+        sys.exit(1)
+
+    if verbose > 0:
+        print "START %s" % ( sys.argv[0].split("/")[-1] )
+        sys.stdout.flush()
+
+    FastaUtils.dbSplit( inFile, nbSeqPerBatch, newDir, useSeqHeader, prefix, verbose )
+
+    if verbose > 0:
+        print "END %s" % ( sys.argv[0].split("/")[-1] )
+        sys.stdout.flush()
+
+    return 0
+
+
+if __name__ == "__main__":
+    main()