def rvscomp(self): self.seq = rvs_comp_str(self.seq)
#!/usr/bin/python
import sys, string
from AshworthUtil import rvs_comp_str
if len(sys.argv) > 1: input = string.join( sys.argv[1:], '' )
else: input = sys.stdin.read()
print rvs_comp_str(input.rstrip('\n'))
def makeprobes(self, fastafiles):
f = FastaSeqs()
f.loadseqs(fastafiles)
print f.summarize()
if self.regions == {}:
for seq in f.seqs.values():
# create region spanning whole seq
l = len(seq)
for d in ["+", "-"]:
self.regions[(seq.name, d)] = {}
ss = RegionSet("noid")
ss.add(Region(seq.name, d, 1, l))
self.regions[(seq.name, d)]["noid"] = ss
else:
# prevent lookup errors
for seq in f.seqs.values():
for d in ["+", "-"]:
if not self.regions.has_key((seq.name, d)):
self.regions[(seq.name, d)] = {"noid": RegionSet()}
for seq in f.seqs.values():
seqlen = len(seq)
sys.stderr.write("%s\n" % seq.name)
seqabbv = re.sub("_", "", seq.name[: min(len(seq.name), 8)])
# the probes are created starting from the 3' end of the region. This makes it easy to create '3'-biased' probe sets of 'n' probes
# forward strand
for regionset in self.regions[(seq.name, "+")].values():
# sys.stderr.write('+:\n%s\n' %str(regionset))
# start with last region (exon), create probes from 3' end until nprobes reached
nprobes_id = 0
for region in reversed(sorted(regionset.regions)):
nprobes_region = 0
cursor = region.end - self.probelength + self.posoffset
# note: strings 0-indexed (i), genome sequences 1-indexed (i+1)
while cursor >= region.start:
if cursor < 0 or cursor + self.probelength >= seqlen:
break
if self.probespergene > 0 and nprobes_id >= self.probespergene:
break
if self.probesperregion > 0 and nprobes_region >= self.probesperregion:
break
probeseq = seq.seq[cursor : cursor + self.probelength]
if not re.search(opt.mask, probeseq): # skip probes containing masked sequence
probename = "%s_%i_+" % (seqabbv, cursor + 1)
p = Probe(start=cursor + 1, strand="+", name=probename, seq=probeseq, parent=seq.name)
self.probes.append(p)
nprobes_id += 1
nprobes_region += 1
cursor -= self.probelength + self.gap
# reverse strand
for regionset in self.regions[(seq.name, "-")].values():
# sys.stderr.write('-:\n%s\n' %str(regionset))
nprobes_id = 0
for region in sorted(regionset.regions):
nprobes_region = 0
cursor = region.start + self.negoffset
while cursor < region.end - self.probelength:
if cursor < 0 or cursor + self.probelength >= seqlen:
break
if self.probespergene > 0 and nprobes_id >= self.probespergene:
break
if self.probesperregion > 0 and nprobes_region >= self.probesperregion:
break
probeseq = seq.seq[cursor : cursor + self.probelength]
if not re.search(opt.mask, probeseq):
probename = "%s_%i_-" % (seqabbv, cursor + 1)
p = Probe(
start=cursor + 1,
strand="-",
name=probename,
seq=rvs_comp_str(probeseq),
parent=seq.name,
)
self.probes.append(p)
nprobes_id += 1
nprobes_region += 1
cursor += self.probelength + self.gap
def makeprobes(self,fastafiles):
f=FastaSeqs()
f.loadseqs(fastafiles)
print f.summarize()
if self.regions == {}:
for seq in f.seqs.values():
# create region spanning whole seq
l = len(seq)
for d in ['+','-']:
self.regions[(seq.name,d)] = {}
ss = RegionSet('noid')
ss.add( Region(seq.name,d,1,l) )
self.regions[ (seq.name,d) ]['noid'] = ss
else:
# prevent lookup errors
for seq in f.seqs.values():
for d in ['+','-']:
if not self.regions.has_key( (seq.name,d) ):
self.regions[ (seq.name,d) ] = {'noid':RegionSet()}
for seq in f.seqs.values():
seqlen = len(seq)
sys.stderr.write('%s\n' %seq.name)
seqabbv=re.sub('_','',seq.name[ : min(len(seq.name),8) ])
# the probes are created starting from the 3' end of the region. This makes it easy to create '3'-biased' probe sets of 'n' probes
# forward strand
for regionset in self.regions[(seq.name,'+')].values():
# sys.stderr.write('+:\n%s\n' %str(regionset))
# start with last region (exon), create probes from 3' end until nprobes reached
nprobes_id = 0
for region in reversed(sorted(regionset.regions)):
nprobes_region = 0
cursor = region.end - self.probelength + self.posoffset
# note: strings 0-indexed (i), genome sequences 1-indexed (i+1)
while cursor >= region.start:
if cursor < 0 or cursor + self.probelength >= seqlen: break
if self.probespergene > 0 and nprobes_id >= self.probespergene: break
if self.probesperregion > 0 and nprobes_region >= self.probesperregion: break
probeseq=seq.seq[cursor:cursor+self.probelength]
if not re.search(opt.mask,probeseq): # skip probes containing masked sequence
probename='%s_%i_+' %(seqabbv,cursor+1)
p=Probe( start=cursor+1, strand='+', name=probename, seq=probeseq, parent=seq.name )
self.probes.append(p)
nprobes_id += 1
nprobes_region += 1
cursor -= self.probelength + self.gap
# reverse strand
for regionset in self.regions[(seq.name,'-')].values():
# sys.stderr.write('-:\n%s\n' %str(regionset))
nprobes_id = 0
for region in sorted(regionset.regions):
nprobes_region = 0
cursor = region.start + self.negoffset
while cursor < region.end - self.probelength:
if cursor < 0 or cursor + self.probelength >= seqlen: break
if self.probespergene > 0 and nprobes_id >= self.probespergene: break
if self.probesperregion > 0 and nprobes_region >= self.probesperregion: break
probeseq=seq.seq[cursor:cursor+self.probelength]
if not re.search(opt.mask,probeseq):
probename='%s_%i_-' %(seqabbv,cursor+1)
p=Probe( start=cursor+1, strand='-', name=probename, seq=rvs_comp_str(probeseq), parent=seq.name )
self.probes.append(p)
nprobes_id += 1
nprobes_region += 1
cursor += self.probelength + self.gap
def countsites(self, seq, length):
n = range(len(seq) - length)
for i in n:
subseq = seq[i:i + length]
self.sites[subseq] += 1
self.sites[rvs_comp_str(subseq)] += 1
def countsites(self,seq,length): n = range(len(seq)-length) for i in n: subseq = seq[i:i+length] self.sites[subseq] += 1 self.sites[rvs_comp_str(subseq)] += 1
if not parent in genes:
genes[parent] = Gene()
genes[parent]['seq'] = seq
genes[parent]['cds'] = []
genes[parent]['cds'].append((start, end, strand))
seqfile = sys.argv[2]
src = FastaSeqs()
src.loadseqs([seqfile])
outp = []
for id, gene in genes.items():
seq = gene['seq']
if not seq in src.seqs:
msg('%s not found in source!' % seq)
sys.exit()
if 'cds' in gene:
fullcds = []
rvs = False
for start, end, strand in sorted(gene['cds'], key=lambda x: x[0]):
ss = src.seqs[seq].seq[(start - 1):end]
if strand == '-':
ss = rvs_comp_str(ss)
rvs = True
fullcds.append(ss)
if rvs: fullcds.reverse()
outp.append('>%s_%s\n%s' % (id, 'cds', ''.join(fullcds)))
print('\n'.join(outp))