--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BlastParser_and_hits.py	Sun Jun 21 14:31:29 2015 -0400
@@ -0,0 +1,177 @@
+#!/usr/bin/python
+#  blastn blastx parser revised debugged: 3-4-2015. Commit issue.
+# drosofff@gmail.com
+
+import sys
+import argparse
+from collections import defaultdict
+
+def Parser():
+    the_parser = argparse.ArgumentParser()
+    the_parser.add_argument('--blast', action="store", type=str, help="Path to the blast output (tabular format, 12 column)")
+    the_parser.add_argument('--sequences', action="store", type=str, help="Path to the fasta file with blasted sequences")
+    the_parser.add_argument('--fastaOutput', action="store", type=str, help="fasta output file of blast hits")
+    the_parser.add_argument('--tabularOutput', action="store", type=str, help="tabular output file of blast analysis")
+    the_parser.add_argument('--flanking', action="store", type=int, help="number of flanking nucleotides added to the hit sequences") 
+    the_parser.add_argument('--mode', action="store", choices=["verbose", "short"], type=str, help="reporting (verbose) or not reporting (short) oases contigs")
+    args = the_parser.parse_args()
+    if not all ( (args.sequences, args.blast, args.fastaOutput, args.tabularOutput) ):
+        the_parser.error('argument(s) missing, call the -h option of the script')
+    if not args.flanking:
+        args.flanking = 0
+    return args
+
+def median(lst):
+    lst = sorted(lst)
+    if len(lst) < 1:
+            return None
+    if len(lst) %2 == 1:
+            return lst[((len(lst)+1)/2)-1]
+    if len(lst) %2 == 0:
+            return float(sum(lst[(len(lst)/2)-1:(len(lst)/2)+1]))/2.0
+
+def mean(lst):
+    if len(lst) < 1:
+        return 0
+    return sum(lst) / float(len(lst))
+
+def getfasta (fastafile):
+    fastadic = {}
+    for line in open (fastafile):
+        if line[0] == ">":
+            header = line[1:-1]
+            fastadic[header] = ""
+        else:
+            fastadic[header] += line
+    for header in fastadic:
+        fastadic[header] = "".join(fastadic[header].split("\n"))
+    return fastadic
+
+def insert_newlines(string, every=60):
+    lines = []
+    for i in xrange(0, len(string), every):
+        lines.append(string[i:i+every])
+    return '\n'.join(lines)
+    
+def getblast (blastfile):
+    '''blastinfo [0]	Percentage of identical matches
+       blastinfo [1]	Alignment length
+       blastinfo [2]	Number of mismatches
+       blastinfo [3]	Number of gap openings
+       blastinfo [4]	Start of alignment in query
+       blastinfo [5]	End of alignment in query
+       blastinfo [6]	Start of alignment in subject (database hit)
+       blastinfo [7]	End of alignment in subject (database hit)
+       blastinfo [8]	Expectation value (E-value)
+       blastinfo [9]	Bit score
+       blastinfo [10]	Subject length (NEED TO BE SPECIFIED WHEN RUNNING BLAST) '''
+    blastdic = defaultdict (dict) 
+    for line in open (blastfile):
+        fields = line[:-1].split("\t")
+        transcript = fields[0]
+        subject = fields[1]
+        blastinfo = [float(fields[2]) ] # blastinfo[0]
+        blastinfo = blastinfo + [int(i) for i in fields[3:10] ] # blastinfo[1:8] insets 1 to 7
+        blastinfo.append(fields[10]) # blastinfo[8] E-value remains as a string type
+        blastinfo.append(float(fields[11])) # blastinfo[9] Bit score
+        blastinfo.append(int(fields[12])) # blastinfo[10] Subject length MUST BE RETRIEVED THROUGH A 13 COLUMN BLAST OUTPUT
+        try:
+            blastdic[subject][transcript].append(blastinfo)
+        except:
+            blastdic[subject][transcript] = [ blastinfo ]
+    return blastdic
+
+def getseq (fastadict, transcript, up, down, orientation="direct"):
+    def reverse (seq):
+        revdict = {"A":"T","T":"A","G":"C","C":"G","N":"N"}
+        revseq = [revdict[i] for i in seq[::-1]]
+        return "".join(revseq)
+    pickseq = fastadict[transcript][up-1:down]
+    if orientation == "direct":
+        return pickseq
+    else:
+        return reverse(pickseq)
+
+def subjectCoverage (fastadict, blastdict, subject, QueriesFlankingNucleotides=0):
+    SubjectCoverageList = []
+    HitDic = {}
+    bitScores = []
+    for transcript in blastdict[subject]:
+        prefix = "%s--%s_" % (subject, transcript)
+        hitNumber = 0
+        for hit in blastdict[subject][transcript]:
+            hitNumber += 1
+            suffix = "hit%s_IdMatch=%s,AligLength=%s,E-val=%s" % (hitNumber, hit[0], hit[1], hit[8])
+            HitDic[prefix+suffix] = GetHitSequence (fastadict, transcript, hit[4], hit[5], QueriesFlankingNucleotides) #query coverage by a hit is in hit[4:6]
+            SubjectCoverageList += range (min([hit[6], hit[7]]), max([hit[6], hit[7]]) + 1) # subject coverage by a hit is in hit[6:8]
+            bitScores.append(hit[9])
+            subjectLength = hit [10] # always the same value for a given subject. Stupid but simple
+    TotalSubjectCoverage = len ( set (SubjectCoverageList) )
+    RelativeSubjectCoverage = TotalSubjectCoverage/float(subjectLength)
+    return HitDic, subjectLength, TotalSubjectCoverage, RelativeSubjectCoverage, max(bitScores), mean(bitScores)
+    
+def GetHitSequence (fastadict, FastaHeader, leftCoordinate, rightCoordinate, FlankingValue):
+    if rightCoordinate > leftCoordinate:
+        polarity = "direct"
+    else:
+        polarity = "reverse"
+        leftCoordinate, rightCoordinate = rightCoordinate, leftCoordinate
+    if leftCoordinate - FlankingValue > 0:
+        leftCoordinate -= FlankingValue
+    else:
+        leftCoordinate = 1
+    return getseq (fastadict, FastaHeader, leftCoordinate, rightCoordinate, polarity)
+    
+def outputParsing (F, Fasta, results, Xblastdict, fastadict, mode="verbose"):
+    F= open(F, "w")
+    Fasta=open(Fasta, "w")
+    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):
+            print >> F, "#\n# %s" % subject
+            print >> F, "# Suject Length: %s" % (results[subject]["subjectLength"])
+            print >> F, "# Total Subject Coverage: %s" % (results[subject]["TotalCoverage"])
+            print >> F, "# Relative Subject Coverage: %s" % (results[subject]["RelativeSubjectCoverage"])
+            print >> F, "# Maximum Bit Score: %s" % (results[subject]["maxBitScores"])
+            print >> F, "# Mean Bit Score: %s" % (results[subject]["meanBitScores"])
+            for header in results[subject]["HitDic"]:
+                print >> Fasta, ">%s\n%s" % (header, insert_newlines(results[subject]["HitDic"][header]) )
+            print >> Fasta, "" # final carriage return for the sequence
+            for transcript in Xblastdict[subject]:
+                transcriptSize = float(len(fastadict[transcript]))
+                for hit in Xblastdict[subject][transcript]:
+                    percentIdentity, alignLenght, subjectStart, subjectEnd, queryCov = hit[0], hit[1], hit[6], hit[7], "%.1f" % (abs(hit[5]-hit[4])/transcriptSize*100)
+                    Eval, BitScore = hit[8], hit[9]
+                    info = [transcript] + [percentIdentity, alignLenght, subjectStart, subjectEnd, queryCov, Eval, BitScore]
+                    info = [str(i) for i in info]
+                    info = "\t".join(info)
+                    print >> F, info
+    else:
+        print >>F, "# subject\tsubject length\tTotal Subject Coverage\tRelative Subject Coverage\tMaximum Bit Score\tMean Bit Score"
+        for subject in sorted (results, key=lambda x: results[x]["meanBitScores"], reverse=True):
+            line = []
+            line.append(subject)
+            line.append(results[subject]["subjectLength"])
+            line.append(results[subject]["TotalCoverage"])
+            line.append(results[subject]["RelativeSubjectCoverage"])
+            line.append(results[subject]["maxBitScores"])
+            line.append(results[subject]["meanBitScores"])
+            line = [str(i) for i in line]
+            print >> F, "\t".join(line)
+            for header in results[subject]["HitDic"]:
+                print >> Fasta, ">%s\n%s" % (header, insert_newlines(results[subject]["HitDic"][header]) )
+            print >> Fasta, "" # final carriage return for the sequence
+    F.close()
+    Fasta.close()
+        
+    
+
+def __main__ ():
+    args = Parser()
+    fastadict = getfasta (args.sequences)
+    Xblastdict = getblast (args.blast)
+    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, args.mode)
+if __name__=="__main__": __main__()