--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/launchBlasterMatcherPerQuery.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,196 @@
+#!/usr/bin/env python
+
+"""
+This program splits the input fasta file in a given number of files, launch Blaster and/or Matcher on them in parallel and collect the results afterwards.
+"""
+
+import os
+import sys
+import getopt
+import exceptions
+import logging
+import ConfigParser
+
+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"] )
+
+import pyRepet.launcher.programLauncher
+import pyRepet.seq.fastaDB
+
+#-----------------------------------------------------------------------------
+
+def help():
+
+    """
+    Give the list of the command-line options.
+    """
+
+    print
+    print "usage:",sys.argv[0]," [ options ]"
+    print "options:"
+    print "     -h: this help"
+    print "     -q: fasta filename of the queries"
+    print "     -s: fasta filename of the subjects (same as queries if not specified)"
+    print "     -Q: queue name on the cluster"
+    print "     -d: absolute path to the temporary directory"
+    print "     -C: configuration file"
+    print "     -n: max. number of jobs (default=10,given a min. of 1 query per job)"
+    print "     -m: mix of Blaster and/or Matcher"
+    print "         1: launch Blaster only"
+    print "         2: launch Matcher only (on '*.align' query files)"
+    print "         3: launch Blaster+Matcher in the same job (default)"
+    print "     -B: parameters for Blaster (e.g. \"-a -n tblastx\")"
+    print "     -M: parameters for Matcher (e.g. \"-j\")"
+    print "     -Z: collect all the results into a single file (format 'align', 'path' or 'tab')"
+    print "     -c: clean"
+    print "     -v: verbose (default=0/1/2)"
+    print
+
+#-----------------------------------------------------------------------------
+
+def main():
+
+    """
+    This program splits the input fasta file in a given number of files, launch Blaster and/or Matcher on them in parallel and collect the results afterwards.
+    """
+
+    qryFileName = ""
+    sbjFileName = ""
+    queue = ""
+    tmpDir = ""
+    configFileName = ""
+    maxNbJobs = 10
+    minQryPerJob = 1
+    mix = "3"
+    paramBlaster = ""
+    paramMatcher = ""
+    collectFormat = ""
+    clean = False
+    verbose = 0
+
+    try:
+        opts, args = getopt.getopt(sys.argv[1:],"hq:s:Q:d:C:n:m:B:M:Z:cv:")
+    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 == "-q":
+            qryFileName = a 
+        elif o == "-s":
+            sbjFileName = a
+        elif o == "-Q":
+            queue = a
+        elif o == "-d":
+            tmpDir = a
+        elif o == "-C":
+            configFileName = a
+        elif o == "-n":
+            maxNbJobs = int(a)
+        elif o == "-m":
+            mix = a
+        elif o == "-B":
+            paramBlaster = a
+        elif o == "-M":
+            paramMatcher = a
+        elif o == "-Z":
+            collectFormat = a
+        elif o == "-c":
+            clean = True
+        elif o == "-v":
+            verbose = int(a)
+
+    if qryFileName == "" or configFileName == "" or collectFormat == "":
+        print "*** Error: missing compulsory options"
+        help()
+        sys.exit(1)
+
+    if verbose > 0:
+        print "\nbeginning of %s" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+
+    if not os.path.exists( qryFileName ):
+        print "*** Error: query file '%s' doesn't exist" % ( qryFileName )
+        sys.exit(1)
+    if sbjFileName != "":
+        if not os.path.exists( sbjFileName ):
+            print "*** Error: subject file '%s' doesn't exist" % ( sbjFileName )
+            sys.exit(1)
+    else:
+        sbjFileName = qryFileName
+
+    pL = pyRepet.launcher.programLauncher.programLauncher()
+
+    nbSeqQry = pyRepet.seq.fastaDB.dbSize( qryFileName )
+    qryPerJob = nbSeqQry / float(maxNbJobs)
+
+    # split the input query file in single files into a new directory
+    prg = os.environ["REPET_PATH"] + "/bin/dbSplit.py"
+    cmd = prg
+    cmd += " -i %s" % ( qryFileName )
+    if qryPerJob <= 1.0:
+        cmd += " -n %i" % ( minQryPerJob )
+    else:
+        cmd += " -n %i" % ( qryPerJob + 1 )
+    cmd += " -d"
+    pL.launch( prg, cmd )
+
+    # prepare the subject databank
+    if sbjFileName != qryFileName:
+        prg = "blaster"
+        cmd = prg
+        cmd += " -q %s" % ( sbjFileName )
+        cmd += " -P"
+        pL.launch( prg, cmd )
+
+    # launch Blaster+Matcher in parallel
+    prg = "srptBlasterMatcher.py"
+    cmd = prg
+    cmd += " -g %s_vs_%s" % ( qryFileName, sbjFileName )
+    cmd += " -q %s/batches" % ( os.getcwd() )
+    cmd += " -s %s/%s" % ( os.getcwd(), sbjFileName )
+    cmd += " -Q '%s'" % ( queue )
+    if tmpDir != "":
+        cmd += " -d %s" % ( tmpDir )
+    cmd += " -m %s" % ( mix )
+    if paramBlaster != "":
+        cmd += " -B \"%s\"" % ( paramBlaster )
+    if paramMatcher != "":
+        cmd += " -M \"%s\"" % ( paramMatcher )
+    cmd += " -Z %s" % ( collectFormat )
+    cmd += " -C %s" % ( configFileName )
+    if clean == True:
+        cmd += " -c"
+    cmd += " -v %i" % ( verbose - 1 )
+    pL.launch( prg, cmd )
+
+    suffix = ""
+    if mix in ["2","3"]:
+        if "-a" in paramMatcher:
+            suffix = "match.%s" % ( collectFormat )
+        else:
+            suffix = "clean_match.%s" % ( collectFormat )
+        os.system( "mv %s_vs_%s.%s %s_vs_%s.align.%s" % ( qryFileName, sbjFileName, collectFormat, qryFileName, sbjFileName, suffix ) )
+
+    # clean
+    if clean == True:
+        prg = "rm"
+        cmd = prg
+        cmd += " -rf batches formatdb.log %s_cut* %s.Nstretch.map" % ( sbjFileName, sbjFileName )
+        pL.launch( prg, cmd )
+
+    if verbose > 0:
+        print "%s finished successfully\n" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+
+    return 0
+
+#----------------------------------------------------------------------------
+
+if __name__ == '__main__':
+    main()