--- a/BlastParser_and_hits.py	Mon Sep 14 12:18:46 2015 -0400
+++ b/BlastParser_and_hits.py	Tue Sep 29 06:32:31 2015 -0400
@@ -130,6 +130,13 @@
 def outputParsing (F, Fasta, results, Xblastdict, fastadict, filter_relativeCov=0, filter_maxScore=0, filter_meanScore=0, mode="verbose"):
     F= open(F, "w")
     Fasta=open(Fasta, "w")
+    blasted_transcripts = []
+    for subject in results:
+        if results[subject]["RelativeSubjectCoverage"]<filter_relativeCov or results[subject]["maxBitScores"]<filter_maxScore or results[subject]["meanBitScores"]<filter_meanScore:
+            continue
+        for transcript in Xblastdict[subject]:
+            blasted_transcripts.append(transcript)
+    blasted_transcripts = list( set( blasted_transcripts))
     if mode == "verbose":
         print >>F, "# SeqId\t%Identity\tAlignLength\tStartSubject\tEndSubject\t%QueryHitCov\tE-value\tBitScore\n"
         for subject in sorted (results, key=lambda x: results[x]["meanBitScores"], reverse=True):
@@ -172,18 +179,14 @@
             print >> Fasta, "" # final carriage return for the sequence
     F.close()
     Fasta.close()
+    return blasted_transcripts
         
-def sort_sequences (fastadict, blastdict, matched_sequences, unmatched_sequences):
+def dispatch_sequences (fastadict, blasted_transcripts, matched_sequences, unmatched_sequences):
     '''to output the sequences that matched and did not matched in the blast'''
-    blasted_transcripts = []
-    for subject in blastdict:
-        for transcript in blastdict[subject]:
-            blasted_transcripts.append(transcript)
-    blasted_transcripts = list( set( blasted_transcripts))
     F_matched = open (matched_sequences, "w")
     F_unmatched = open (unmatched_sequences, "w")
     for transcript in fastadict:
-        if transcript in blasted_transcripts:
+        if transcript in blasted_transcripts: # le list of blasted_transcripts is generated by the outputParsing function
             print >> F_matched, ">%s\n%s" % (transcript, insert_newlines(fastadict[transcript]) )
         else:
             print >> F_unmatched, ">%s\n%s" % (transcript, insert_newlines(fastadict[transcript]) )
@@ -195,11 +198,12 @@
     args = Parser()
     fastadict = getfasta (args.sequences)
     Xblastdict = getblast (args.blast)
-    sort_sequences (fastadict, Xblastdict, args.al_sequences, args.un_sequences)
     results = defaultdict(dict)
     for subject in Xblastdict:
         results[subject]["HitDic"], results[subject]["subjectLength"], results[subject]["TotalCoverage"], results[subject]["RelativeSubjectCoverage"], results[subject]["maxBitScores"], results[subject]["meanBitScores"]  = subjectCoverage(fastadict, Xblastdict, subject, args.flanking)
-    outputParsing (args.tabularOutput, args.fastaOutput, results, Xblastdict, fastadict,
-                  filter_relativeCov=args.filter_relativeCov, filter_maxScore=args.filter_maxScore,
-                  filter_meanScore=args.filter_meanScore, mode=args.mode)
+    blasted_transcripts = outputParsing (args.tabularOutput, args.fastaOutput, results, Xblastdict, fastadict,
+                                        filter_relativeCov=args.filter_relativeCov, filter_maxScore=args.filter_maxScore,
+                                        filter_meanScore=args.filter_meanScore, mode=args.mode)
+    dispatch_sequences (fastadict, blasted_transcripts, args.al_sequences, args.un_sequences)
+
 if __name__=="__main__": __main__()