def lancetBlastnGeneIntron(): repGenome = "/Users/afutil/Documents/Genolevures/PiFa/Annotation/PourPascal/tBlastNPisoIntron" allfile = glob.glob("%s/ProtIntron/*.tfa" % repGenome) #outdir1 = "%s/tBlastn" % repGenome outdir2 = "%s/tBlastnFmt6" % repGenome #db1 = "%s/DBblast/pifaScaff" % repGenome db2 = "%s/DBblast/pifaScaffFmt6" % repGenome #print "outdir1 = %s, db1 = %s" % (outdir1,db1) for file in allfile: # print "--%s--" % file #outfile1 = "%s/%s.tblastn" % (outdir1,files.get_name(file).lower()) #if not os.path.isfile(outfile1): # print "++%s++" % outfile1 # alignement.run_tblastn(file,outfile1,db1) #else: # print "outfile1 exists" outfile2 = "%s/%s.tblastn" % (outdir2,files.get_name(file).lower()) if not os.path.isfile(outfile2): print "++%s++" % outfile2 alignement.run_tblastnFmt(file,outfile2,db2) else: print "outfile2 exists"
def lanceRechercheSimInc(file,repOut,db): #outfile = "%s/%s-11strains.tblastn" % (repOut,files.get_name(file)) #outfileB = "%s/%s-11strains-Fmt6.tblastn" % (repOut,files.get_name(file)) outfile = "%s/%s-4strains.tblastn" % (repOut,files.get_name(file)) outfileB = "%s/%s-4strains-Fmt6.tblastn" % (repOut,files.get_name(file)) if not os.path.isfile(outfile): alignement.run_tblastn(file,outfile,db) else: print "%s exists" % outfile if not os.path.isfile(outfileB): alignement.run_tblastnFmt(file,outfileB,db) else: print "%s exists" % outfileB return outfileB
def lanceFullBlast(repGenome): allfile = glob.glob("/Users/afutil/Documents/Genolevures/Sace/Fasta/*.tfa") outdir1 = "%s/tBlastN-Sace/" % repGenome outdir2 = "%s/tBlastNFmt6-Sace/" % repGenome db1 = "%s/ScaffTfa/DBblast/pifaGen" % repGenome #db2 = "%s/ScaffTfa/DBblast/pifaGenForFmt" % repGenome print "outdir1 = %s, db1 = %s" % (outdir1,db1) for file in allfile: print "--%s--" % file outfile1 = "%s/%s.tblastn" % (outdir1,files.get_name(file).lower()) if not os.path.isfile(outfile1): print "++%s++" % outfile1 alignement.run_tblastn(file,outfile1,db1) else: print "outfile1 exists" outfile2 = "%s/%s.tblastn" % (outdir2,files.get_name(file).lower()) if not os.path.isfile(outfile2): print "++%s++" % outfile2 alignement.run_tblastnFmt(file,outfile2,db1) else: print "outfile2 exists"