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
