def getBlastScoreRatios(pathQuery, pathReference, pathDB, allelescores, blast_out_file, countQueries):
fileNamequery = os.path.basename(pathQuery)
dirNamequery = os.path.dirname(pathQuery)
translatedqueryFile_path = Translate_FASTA(pathQuery, os.path.join(dirNamequery, fileNamequery + '_translatedSequences.fasta'))
dirNameref = os.path.dirname(pathReference)
fileNameref = os.path.basename(pathReference)
translatedreferenceFile_path = Translate_FASTA(pathReference, os.path.join(dirNameref, fileNameref + str(countQueries) + '_translatedSequences.fasta'))
cline = run_BLAST(translatedreferenceFile_path, pathDB, translatedqueryFile_path, True, blast_out_file)
allelescore = 0
blast_records = runBlastParser( blast_out_file, "")
bestmatch = ""
bestmatchArray = {}
for blast_record in blast_records:
bestmatchArray[str(blast_record.query)] = []
for alignment in blast_record.alignments:
for match in alignment.hsps:
blastScoreRatio = float(match.score) / float(allelescores[str(alignment.hit_def)])
cdsStrName=blast_record.query
if blastScoreRatio > 0:
bestmatchArray[str(blast_record.query)].append([str(alignment.hit_def), str(match.score), str(blastScoreRatio)])
break
return bestmatchArray
def getOwnBlastScore(FASTAfile, dbName, blast_out_file):
fileName = os.path.basename(FASTAfile)
dirName = os.path.dirname(FASTAfile)
translatedFile_path = Translate_FASTA(FASTAfile, os.path.join(dirName, fileName + '_translatedSequences.fasta'))
cline = run_BLAST(translatedFile_path, dbName, translatedFile_path, True, blast_out_file)
os.remove(translatedFile_path)
blast_records = runBlastParser(blast_out_file, "")
allelescores = {}
totalBestMatches = {}
for blast_record in blast_records:
found=False
queryName = blast_record.query
bestmatches = {}
for alignment in blast_record.alignments:
if found is False:
for match in alignment.hsps:
try:
if allelescores[str(alignment.hit_def)] < match.score:
allelescores[str(alignment.hit_def)] = int(match.score)
break
except KeyError:
allelescores[str(alignment.hit_def)] = int(match.score)
break
else:
break
return allelescores
