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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/FilterAlign.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,149 @@
+#!/usr/bin/env python
+
+import sys
+import getopt
+import os
+
+
+def help():
+    print
+    print "usage: ",sys.argv[0].split("/")[-1],"[ options ]"
+    print "options:"
+    print "     -h: this help"
+    print "     -i: name of the input file (format='align')"
+    print "     -E: maximum E-value (default=100)"
+    print "     -S: minimum score (default=0)"
+    print "     -I: minimum identity (default=0)"
+    print "     -l: minimum length (default=0)"
+    print "     -L: maximum length (default=1000000000)"
+    print "     -o: name of the output file (default=inFileName+'.filtered')"
+    print "     -v: verbose (default=0/1)"
+    print
+    
+    
+def main():
+    """
+    This program filters the output from BLASTER ('align' file recording HSPs).
+    """
+    
+    inFileName = ""
+    outFileName = ""
+    maxEValue = 100
+    minIdentity = 0
+    minLength = 0
+    maxLength = 1000000000
+    minScore = 0
+    verbose = 0
+    
+    try:
+        opts, args = getopt.getopt(sys.argv[1:],"hi:E:S:I:l:L:o:v:")
+    except getopt.GetoptError, err:
+        print str(err)
+        help()
+        sys.exit(1)
+    for o,a in opts:
+        if o == "-h":
+            help()
+            sys.exit()
+        elif o == "-i":
+            inFileName = a
+        elif o == "-E":
+            maxEValue = float(a)
+        elif o == "-S":
+            minScore = int(float(a))
+        elif o == "-I":
+            minIdentity = int(float(a))
+        elif o == "-l":
+            minLength = int(a)
+        elif o == "-L":
+            maxLength = int(a)
+        elif o == "-o":
+            outFileName = a
+        elif o == "-v":
+            verbose = int(a)
+            
+    if inFileName == "":
+        print "ERROR: missing input file name"
+        help()
+        sys.exit(1)
+        
+    if outFileName == "":
+        outFileName = "%s.filtered" % ( inFileName )
+        
+    if os.path.exists( os.environ["REPET_PATH"] + "/bin/filterAlign" ):
+        prg = os.environ["REPET_PATH"] + "/bin/filterAlign"
+        cmd = prg
+        cmd += " -i %s" % ( inFileName )
+        cmd += " -E %g" % ( maxEValue )
+        cmd += " -S %i" % ( minScore )
+        cmd += " -I %f" % ( minIdentity )
+        cmd += " -l %i" % ( minLength )
+        cmd += " -L %i" % ( maxLength )
+        cmd += " -o %s" % ( outFileName )
+        cmd += " -v %i" % ( verbose )
+        return os.system( cmd )
+    
+    if verbose > 0:
+        print "START %s" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+        
+    inFile = open( inFileName, "r" )
+    outFile = open( outFileName, "w" )
+    
+    nbMatches = 0
+    nbFiltered = 0
+    
+    line = inFile.readline()
+    while True:
+        if line == "":
+            break
+        nbMatches += 1
+        data = line.split("\t")
+        qryName = data[0]
+        qryStart = data[1]
+        qryEnd = data[2]
+        sbjName = data[3]
+        sbjStart = data[4]
+        sbjEnd = data[5]
+        Evalue = data[6]
+        score = data[7]
+        identity = data[8]
+        
+        if int(qryStart) < int(qryEnd):
+            matchLength = int(qryEnd) - int(qryStart) + 1
+        elif int(qryStart) > int(qryEnd):
+            matchLength = int(qryStart) - int(qryEnd) + 1
+
+        if float(Evalue) <= maxEValue and matchLength >= minLength and \
+               float(identity) >= minIdentity and matchLength <= maxLength and \
+               int(score) >= minScore:
+            string = qryName + "\t" + qryStart + "\t" + qryEnd + "\t" +\
+                     sbjName + "\t" + sbjStart + "\t" + sbjEnd + "\t" +\
+                     Evalue + "\t" + score + "\t" + identity
+            outFile.write( string )
+        else:
+            nbFiltered += 1
+            string = "qry %s (%s-%s) vs subj %s (%s-%s): Eval=%s identity=%s matchLength=%s score=%s" %\
+            ( qryName, qryStart, qryEnd, sbjName, sbjStart, sbjEnd, Evalue, identity.split("\n")[0], matchLength, score )
+            if verbose > 1:
+                print string; sys.stdout.flush()
+                
+        line = inFile.readline()
+        
+    inFile.close()
+    outFile.close()
+    
+    if verbose > 0:
+        msg = "total number of matches: %i" % ( nbMatches )
+        msg += "\nnumber of filtered matches: %i" % ( nbFiltered )
+        print msg; sys.stdout.flush()
+        
+    if verbose > 0:
+        print "END %s" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+        
+    return 0
+
+
+if __name__ == "__main__":
+    main()