diff commons/tools/dbBestLength.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/dbBestLength.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+
+## @file
+# This program extracts the n longest sequences from the input fasta file.
+# usage: dbBestLength.py [ options ]
+# options:
+#      -h: this help
+#      -i: name of the input fasta file
+#      -n: maximum number of sequences in the output file (default=20)
+#      -o: name of the output fasta file (default=inFileName+'.best20')
+#      -v: verbose (default=0/1/2)
+
+import os
+import sys
+import getopt
+
+if not os.environ.has_key( "REPET_PATH" ):
+    print "*** Error: no environment variable REPET_PATH"
+    sys.exit(1)
+sys.path.append( os.environ["REPET_PATH"] )
+
+from pyRepet.seq.fastaDB import * 
+
+
+def help():
+    """
+    Give the list of the command-line options.
+    """
+    print
+    print "usage: dbBestLength.py [ options ]"
+    print "options:"
+    print "     -h: this help"
+    print "     -i: name of the input fasta file"
+    print "     -n: maximum number of sequences in the output file (default=20)"
+    print "     -o: name of the output fasta file (default=inFileName+'.best20')"
+    print "     -v: verbose (default=0/1/2)"
+    print
+
+
+def main():
+    """
+    This program extracts the n longest sequences from the input fasta file.
+    """
+
+    inFileName = ""
+    nbSeq = 20
+    outFileName = ""
+    verbose = 0
+
+    try:
+        opts, args = getopt.getopt(sys.argv[1:],"hi:n:o:v:")
+    except getopt.GetoptError, err:
+        print str(err)
+        help()
+        sys.exit(1)
+    for o,a in opts:
+        if o == "-h":
+            help()
+            sys.exit(0)
+        elif o == "-i":
+            inFileName = a
+        elif o == "-n":
+            nbSeq = a
+        elif o == "-o":
+            outFileName = a
+        elif o == "-v":
+            verbose = int(a)
+
+    if  inFileName == "":
+        print "ERROR: missing input file (-i)"
+        help()
+        sys.exit(1)
+
+    if verbose > 0:
+        print "START dbBestLength.py"
+        sys.stdout.flush()
+
+    if outFileName == "":
+        outFileName = "%s.best%s" % ( inFileName, nbSeq )
+
+    log = dbBestLength( nbSeq, inFileName, outFileName, verbose )
+    if log != 0:
+        print "ERROR: dbBestLength() returned %i" % ( log )
+        sys.exit(1)
+
+    if verbose > 0:
+        print "END dbBestLength.py"
+        sys.stdout.flush()
+
+    return 0
+
+
+if __name__ == "__main__":
+    main()