pattern = re.compile('[\*|X{200,}]')
minLen = 20
i = 0
writer = fasta.MfaWriter('ORFs.fa')
filename = sys.argv[1]
header,dna = fasta.load(filename)
header = header.strip()
orfIter = sequence.extractOrfsIter(dna, minLen=minLen, pattern=pattern)
for i,gStart,gEnd,orf in orfIter:
h = '%s.%i.%i-%i Length=%i' % (header,i,gStart,gEnd,len(orf))
writer.write(h, orf)
fasta.pretty(h, orf)
if gStart<gEnd:
s = dna[gStart-1:gEnd]
print gStart, gEnd, len(s), len(s) % 3==0
print sequence.codons(s, remainder=True)
print sequence.translate(s)
else:
gStart,gEnd = gEnd,gStart
s = dna[gStart-1:gEnd]
s = sequence.reverseComplement(s)
print gStart, gEnd, len(s), len(s) % 3==0
print sequence.codons(s, remainder=True)
print sequence.translate(s)
print
action="store_true",
dest="complement",
help="Complement sequence",
default=False)
parser.add_option(
"-b", "--reverseComplement", "--revComp",
action="store_true",
dest="reverseComplement",
help="Reverse complement sequence", default=False)
options, args = parser.parse_args(sys.argv)
iFilename = args[1]
start = int(args[2])
end = int(args[3])
header,seq = fasta.load(iFilename)
s = seq[start-1:end]
h = '%s %i-%i' % (header,start,end)
if options.reverse:
s = sequence.reverse(s)
h += '(r)'
elif options.complement:
s = sequence.complement(s)
h += '(c)'
elif options.reverseComplement:
s = sequence.reverse_complement(s)
h += '(rc)'
fasta.pretty(h, s, width=options.width)
pattern = re.compile('[\*|X{200,}]')
minLen = 20
i = 0
writer = fasta.MfaWriter('ORFs.fa')
filename = sys.argv[1]
header, dna = fasta.load(filename)
header = header.strip()
orfIter = sequence.extractOrfsIter(dna, minLen=minLen, pattern=pattern)
for i, gStart, gEnd, orf in orfIter:
h = '%s.%i.%i-%i Length=%i' % (header, i, gStart, gEnd, len(orf))
writer.write(h, orf)
fasta.pretty(h, orf)
if gStart < gEnd:
s = dna[gStart - 1:gEnd]
print gStart, gEnd, len(s), len(s) % 3 == 0
print sequence.codons(s, remainder=True)
print sequence.translate(s)
else:
gStart, gEnd = gEnd, gStart
s = dna[gStart - 1:gEnd]
s = sequence.reverseComplement(s)
print gStart, gEnd, len(s), len(s) % 3 == 0
print sequence.codons(s, remainder=True)
print sequence.translate(s)
print
help="Complement sequence",
default=False)
parser.add_option("-b",
"--reverseComplement",
"--revComp",
action="store_true",
dest="reverseComplement",
help="Reverse complement sequence",
default=False)
options, args = parser.parse_args(sys.argv)
iFilename = args[1]
start = int(args[2])
end = int(args[3])
header, seq = fasta.load(iFilename)
s = seq[start - 1:end]
h = '%s %i-%i' % (header, start, end)
if options.reverse:
s = sequence.reverse(s)
h += '(r)'
elif options.complement:
s = sequence.complement(s)
h += '(c)'
elif options.reverseComplement:
s = sequence.reverse_complement(s)
h += '(rc)'
fasta.pretty(h, s, width=options.width)
