def lanceFullBlast(): inrep = "/Users/afutil/Documents/Genolevures/PiSo/AnalyseGenome/variantUnique+meiose/Meiose/SGD" allfile = glob.glob("%s/*.tfa" % inrep) outdir = "/Users/afutil/Documents/Genolevures/PiSo/AnalyseGenome/variantUnique+meiose/Meiose/SGD" db = "/Users/afutil/Documents/Genolevures/PiSo/SeqFinales/FastaProt/DBblast/pisoProt" print "rep = %s, outdir = %s, db = %s" % (inrep,outdir,db) for file in allfile: print "--%s--" % file outfile = "%s/%s.blastp" % (outdir,files.get_name(file).lower()) if not os.path.isfile(outfile): print "++%s++" % outfile alignement.run_blastp(file,outfile,db) else: print "outfile exists"
def lanceAutoblastP(): repSeq = "/Users/afutil/Documents/Genolevures/Piso/AnalyseGenome/variantUnique+meiose" allfile = glob.glob("%s/1VarTfa/PISO*.tfa" % repSeq) outdir = "%s/1VarAutoBlastp" % repSeq db = "/Users/afutil/Documents/Genolevures/Piso/SeqFinales/FastaProt/DBblast/Piso0.aa" print "outdir = %s, db = %s" % (outdir, db) for file in allfile: print "--%s--" % file outfile = "%s/%s.blastp" % (outdir, files.get_name(file).lower()) outfileB = "%s/%s-Fmt6.blastp" % (outdir, files.get_name(file).lower()) if not os.path.isfile(outfile): # print "++%s++" % outfile1 alignement.run_blastp(file, outfile, db) else: print "%s exists" % outfile if not os.path.isfile(outfileB): # print "++%s++" % outfile1B alignement.run_blastpFmt6(file, outfileB, db) else: print "%s exists" % outfileB
def blastPContreSace(): repGenome = "/Users/afutil/Documents/Genolevures/Pifa/Annotation/ModelGenes/ProtJigsaw/" allfile = glob.glob("%s/*.tfa" % repGenome) outdir1 = "%s/Blastp/ContreSace" % repGenome db1 = "/Users/afutil/Documents/Genolevures/Sace/DBblast/yeast_nrpep.fasta" print "outdir1 = %s, db1 = %s" % (outdir1,db1) for file in allfile: print "--%s--" % file outfile1 = "%s/%s.blastp" % (outdir1,files.get_name(file).lower()) outfile1B = "%s/%s-Fmt6.blastp" % (outdir1,files.get_name(file).lower()) if not os.path.isfile(outfile1): #print "++%s++" % outfile1 alignement.run_blastp(file,outfile1,db1) else: print "%s exists" % outfile1 if not os.path.isfile(outfile1B): #print "++%s++" % outfile1B alignement.run_blastpFmt6(file,outfile1B,db1) else: print "%s exists" % outfile1B
def blastPContrePis(): repGenome = "/Users/afutil/Documents/Genolevures/Pifa/Annotation/ModelGenes/ProtJigsaw/" allfile = glob.glob("%s/*.tfa" % repGenome) outdir1 = "%s/Blastp/ContrePiso/Eq1n" % repGenome outdir2 = "%s/Blastp/ContrePist/CGOB" % repGenome db1 = "/Users/afutil/Documents/Genolevures/Piso/SeqFinales/FastaProt/DBblast/Piso01n.aa" db2 = "/Users/afutil/Documents/Genolevures/Pist/DBblast/allProtPistCGOB.tfa" print "outdir1 = %s, db1 = %s" % (outdir1,db1) for file in allfile: print "--%s--" % file outfile1 = "%s/%s.blastp" % (outdir1,files.get_name(file).lower()) outfile1B = "%s/%s-Fmt6.blastp" % (outdir1,files.get_name(file).lower()) if not os.path.isfile(outfile1): #print "++%s++" % outfile1 alignement.run_blastp(file,outfile1,db1) else: print "%s exists" % outfile1 if not os.path.isfile(outfile1B): #print "++%s++" % outfile1B alignement.run_blastpFmt6(file,outfile1B,db1) else: print "%s exists" % outfile1B outfile2 = "%s/%s.blastp" % (outdir2,files.get_name(file).lower()) outfile2B = "%s/%s-Fmt6.blastp" % (outdir2,files.get_name(file).lower()) if not os.path.isfile(outfile2): #print "++%s++" % outfile2 alignement.run_blastp(file,outfile2,db2) else: print "%s exists" % outfile2 if not os.path.isfile(outfile2B): #print "++%s++" % outfile2B alignement.run_blastpFmt6(file,outfile2B,db2) else: print "%s exists" % outfile2B