if os.path.isfile(sys.argv[1]):
infile = open(sys.argv[1])
dataF = infile.read()
else:
print "file does not exist or can't be opened"
exit()
if os.path.isfile(sys.argv[2]):
infile = open(sys.argv[2])
dataG = infile.read()
else:
print "file does not exist or can't be opened"
exit()
gffb = GFFBlaster(dataF, dataG)
parseDir = sys.argv[3]
nFiles = len(glob.glob(parseDir + "\\" + "*.xml"))
nSeqs = len(glob.glob(parseDir + "\\" + "my_blast-seq-*-gene-0.xml"))
# nGenes = len(glob.glob(sys.argv[3] + "\\" + "my_blast-seq-" + str(0) + "-gene-*.xml"))
nGenes = []
for i in range(nSeqs):
nGenes = nGenes + [len(glob.glob(parseDir + "\\" + "my_blast-seq-" + str(i) + "-gene-*.xml"))]
print "Blast record title of:"
for i in range(nSeqs):
for j in range(nGenes[i]):
from GFFBlaster import GFFBlaster
import sys
import os.path
if os.path.isfile(sys.argv[1]):
infile = open(sys.argv[1])
dataF = infile.read();
else:
print 'file does not exist or can\'t be opened'
exit()
if os.path.isfile(sys.argv[2]):
infile = open(sys.argv[2])
dataG = infile.read();
else:
print 'file does not exist or can\'t be opened'
exit()
gffb = GFFBlaster(dataF , dataG);
def fill(text, width=70):
return '\n'.join(text[i:i+width] for i in
range(0, len(text), width))
for i in range(gffb.getNumberOfSeqs()):
for j in range(gffb.getNumberOfGenesInSeq(i)):
print ">gi|"+sys.argv[1]+"|Gene "+ str(j)+ " of contig " + str(i)
print fill(gffb.getGene(i,j),80)