def runGenomescan(features, debug=False):
"""Run genomescan supplying extracted features from genome as
homologous proteins."""
for i,feature in enumerate(features):
print i+1, feature
oFilename = 'gsOutput/%s.html' % feature.domain
annotFilename = 'gsAnnotations/%s.txt' % feature.domain
pepFilename = 'gsPeptides/%s.fa' % feature.domain
if not os.path.exists(oFilename):
html = genomescanFromFeature(feature, blastDb, oFileHandle=oFilename)
else:
html = open(oFilename).read()
html = html.split('\n')
annotation, peptides = parseGenomeScanOutput(html)
print >> open(annotFilename, 'w'), annotation
fakeFaFile = StringIO.StringIO(peptides)
faIter = fasta.load_iter(fakeFaFile)
writer = fasta.MfaWriter(pepFilename)
for j,(h,s) in enumerate(faIter):
block = h.split('|')[0]
if j==1: print feature
h = '%s.%i %s' % (feature.domain, j+1, block)
writer.write(h, s+'\n')
writer.close()
def runGenomescan(features, debug=False):
"""Run genomescan supplying extracted features from genome as
homologous proteins."""
for i, feature in enumerate(features):
print i + 1, feature
oFilename = 'gsOutput/%s.html' % feature.domain
annotFilename = 'gsAnnotations/%s.txt' % feature.domain
pepFilename = 'gsPeptides/%s.fa' % feature.domain
if not os.path.exists(oFilename):
html = genomescanFromFeature(feature,
blastDb,
oFileHandle=oFilename)
else:
html = open(oFilename).read()
html = html.split('\n')
annotation, peptides = parseGenomeScanOutput(html)
print >> open(annotFilename, 'w'), annotation
fakeFaFile = StringIO.StringIO(peptides)
faIter = fasta.load_iter(fakeFaFile)
writer = fasta.MfaWriter(pepFilename)
for j, (h, s) in enumerate(faIter):
block = h.split('|')[0]
if j == 1: print feature
h = '%s.%i %s' % (feature.domain, j + 1, block)
writer.write(h, s + '\n')
writer.close()
#!/usr/bin/env python
"""
orfTest.py
Author: Tony Papenfuss
Date: Tue Aug 22 20:14:57 EST 2006
"""
import os, sys
import fasta, sequence
header,seq = fasta.load('NKC.fa')
orfIterator = fasta.load_iter('ORFs.fa')
writer = fasta.MfaWriter('ORFs2.fa')
for h,orf in orfIterator:
chrom,block,orfId,limits = h.split()[0].split('.')
start,end = limits.split('-')
start = int(start)
end = int(end)
if start>end:
strand = '-'
start,end = end,start
s = sequence.translate(sequence.reverseComplement(seq[start-1:end]))
else:
strand = '+'
s = sequence.translate(seq[start-1:end])
Author: Tony Papenfuss
Date: Wed Aug 23 08:52:58 EST 2006
"""
import os, sys
import re, copy
import fasta, sequence, hmmer3
from hmmer3 import hmmer2frame
pattern = re.compile('[\*|X{200,}]')
minLen = 20
i = 0
writer = fasta.MfaWriter('ORFs.fa')
faFile = fasta.load_iter('6frames.fa')
for header, seq in faFile:
header = header.strip()
print >> sys.stderr, header
block, hmmerFrame = header.split(':')
frame = hmmer2frame[int(hmmerFrame)]
matchIter = pattern.finditer(seq)
try:
match = matchIter.next()
except StopIteration:
print match
print seq
sys.exit()
start = match.start()
def getSizes(filenames):
for filename in filenames:
for h, s in fasta.load_iter(filename):
name = h.split()[0]
L = len(s)
print '%s\t%s' % (name, L)
writer.write('%s:%i' % (header,frame),p)
writer.close()
sys.exit()
# Initialize()
header,seq = fasta.load('MHC_hg18.fa')
L = len(seq)
hstart = header.split()[0]
pattern = re.compile('\*|X{200,}')
minLen = 20
# sixFrameIter = sequence.sixFrameTranslationIter(seq)
sixFrameIter = fasta.load_iter('6frames.fa')
writer = fasta.MfaWriter('ORFs.fa')
i = 0
for h,p in sixFrameIter:
hmmerFrame = int(h.split(':')[-1])
frame = hmmer.hmmer2frame[hmmerFrame]
print >> sys.stderr, 'Frame:', frame
if frame>0:
strand = '+'
else:
strand = '-'
matchIter = pattern.finditer(p)
match = matchIter.next()
start = match.start()
writer.write('%s:%i' % (header, frame), p)
writer.close()
sys.exit()
# Initialize()
header, seq = fasta.load('MHC_hg18.fa')
L = len(seq)
hstart = header.split()[0]
pattern = re.compile('\*|X{200,}')
minLen = 20
# sixFrameIter = sequence.sixFrameTranslationIter(seq)
sixFrameIter = fasta.load_iter('6frames.fa')
writer = fasta.MfaWriter('ORFs.fa')
i = 0
for h, p in sixFrameIter:
hmmerFrame = int(h.split(':')[-1])
frame = hmmer.hmmer2frame[hmmerFrame]
print >> sys.stderr, 'Frame:', frame
if frame > 0:
strand = '+'
else:
strand = '-'
matchIter = pattern.finditer(p)
match = matchIter.next()
start = match.start()
Date: Wed Aug 23 08:52:58 EST 2006
"""
import os, sys
import re, copy
import fasta, sequence, hmmer3
from hmmer3 import hmmer2frame
pattern = re.compile('[\*|X{200,}]')
minLen = 20
i = 0
writer = fasta.MfaWriter('ORFs.fa')
faFile = fasta.load_iter('6frames.fa')
for header,seq in faFile:
header = header.strip()
print >> sys.stderr, header
block,hmmerFrame = header.split(':')
frame = hmmer2frame[int(hmmerFrame)]
matchIter = pattern.finditer(seq)
try:
match = matchIter.next()
except StopIteration:
print match
print seq
sys.exit()
start = match.start()
def getSizes(filenames):
for filename in filenames:
for h,s in fasta.load_iter(filename):
name = h.split()[0]
L = len(s)
print '%s\t%s' % (name,L)
