def lanceFullBlastFmt(repGenome):
allfile = glob.glob("%s/Proteome-Pist/*.tfa" % repGenome)
outdir = "%s/tBlastNFmt6-Pist/" % repGenome
db = "%s/ScaffTfa/DBblast/pifaGenForFmt" % repGenome
print "outdir = %s, db = %s" % (outdir,db)
for file in allfile:
print "--%s--" % file
outfile = "%s/%s.tblastn" % (outdir,files.get_name(file).lower())
if not os.path.isfile(outfile):
print "++%s++" % outfile
alignement.run_tblastn(file,outfile,db)
else:
print "outfile 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"
