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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/srptPhyML.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,165 @@
+#!/usr/bin/env python
+
+import user, os, sys, getopt, exceptions, logging, 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.sql.RepetJobMySQL
+import pyRepet.launcher.Launcher
+
+#-----------------------------------------------------------------------------
+
+def help():
+
+    """
+    Give the list of the command-line options.
+    """
+
+    print
+    print "usage:",sys.argv[0]," [ options ]"
+    print "options:"
+    print "     -h: this help"
+    print "     -g: name of the group identifier (same for all the jobs)"
+    print "     -q: name of the query directory"
+    print "     -S: suffix in the query directory  (default='*.fa')"
+    print "     -Q: name of the queue (on the cluster)"
+    print "     -d: absolute path to the temporary directory"
+    print "     -C: configuration file from TEdenovo or TEannot pipeline"
+    print "     -t: job table name (default=jobs)"
+    print "     -p: absolute path to project directory (if jobs management via files)"
+    print "     -c: clean (remove job launch files and job stdout)"
+    print "     -v: verbose (default=0/1/2)"
+    print
+
+#-----------------------------------------------------------------------------
+
+def main():
+
+    """
+    This program takes a directory as input and launches MAP on each file in it.
+    """
+
+    groupid = ""
+    queryDir = ""
+    patternSuffix = "*.fa"
+    queue = ""
+    tmpDir = ""
+    configFileName = ""
+    jobTable = "jobs"
+    projectDir = ""
+    clean = False
+    verbose = 0
+
+    try:
+        opts, args = getopt.getopt(sys.argv[1:],"hg:q:S:Q:d:C:t:p: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 == "-g":
+            groupid = a
+        elif o == "-q":
+            queryDir = a
+        elif o == "-S":
+            patternSuffix = a
+        elif o == "-Q":
+            queue = a
+        elif o == "-d":
+            tmpDir = a
+        elif o == "-C":
+            configFileName = a
+        elif o == "-t":
+            jobTable = a
+        elif o == "-p":
+            projectDir = a
+        elif o == "-c":
+            clean = True
+        elif o == "-v":
+            verbose = int(a)
+
+    if  groupid == "" or queryDir == "":
+        print "*** Error: missing compulsory options"
+        help()
+        sys.exit(1)
+
+    if os.environ["REPET_JOBS"] == "files" and projectDir == "":
+        print "*** Error: missing compulsory options for jobs management via files"
+        help()
+        sys.exit(1)
+
+    if verbose > 0:
+        print "\nbeginning of %s" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+
+    #--------------------------------------------------------------------------
+
+    # create the 'log' file
+
+    logFileName = "%s_pid%s.log" % ( groupid, os.getpid() )
+    handler = logging.FileHandler( logFileName )
+    formatter = logging.Formatter( "%(asctime)s %(levelname)s: %(message)s" )
+    handler.setFormatter( formatter )
+    logging.getLogger('').addHandler( handler )
+    logging.getLogger('').setLevel( logging.DEBUG )
+    logging.info( "started" )
+
+
+    # open a connection to the MySQL table
+
+    if configFileName != "":
+        if not os.path.exists( configFileName ):
+            print "*** Error: configuration file '%s' doesn't exist" % ( configFileName )
+            sys.exit(1)
+        config = ConfigParser.ConfigParser()
+        config.readfp( open(configFileName) )
+        host = config.get("repet_env","repet_host")
+        user = config.get("repet_env","repet_user")
+        passwd = config.get("repet_env","repet_pw")
+        dbname = config.get("repet_env","repet_db")
+    else:
+        host = os.environ["REPET_HOST"]
+        user = os.environ["REPET_USER"]
+        passwd = os.environ["REPET_PW"]
+        dbname = os.environ["REPET_DB"]
+
+    if os.environ["REPET_JOBS"] == "files":
+        jobdb = pyRepet.sql.RepetJobMySQL.RepetJob( dbname = projectDir + "/" + os.environ["REPET_DB"] )
+    elif os.environ["REPET_JOBS"] == "MySQL":
+        jobdb = pyRepet.sql.RepetJobMySQL.RepetJob( user, host, passwd, dbname )
+    else:
+        print "*** Error: REPET_JOBS is '%s'" % ( os.environ["REPET_JOBS"] )
+        sys.exit(1)
+
+
+    currentDir = os.getcwd()
+    if tmpDir == "":
+        tmpDir = currentDir
+
+    # launch PhyML on each fasta file in queryDir
+    cL = pyRepet.launcher.Launcher.PhyMlLauncher( jobdb=jobdb, query=queryDir, cdir=currentDir, tmpdir=tmpDir, job_table=jobTable, queue=queue, groupid=groupid, acro="PhyML" )
+    cL.run( patternSuffix )
+
+    # clean
+    if clean == True:
+        cL.clean()
+
+
+    logging.info( "finished" )
+
+    if verbose > 0:
+        print "%s finished successfully\n" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+
+    return 0
+
+#----------------------------------------------------------------------------
+
+if __name__ == '__main__':
+    main()