def _blast_feature(self, f, c1, c2):
trans = Translator(self._abort_event)
cds = trans.translate(f.extract(c1), 11)
sixframes = trans.translate_six_frames_single(c2, 11)
if not sixframes: return [(None, None, None)]
results = []
for frame in sixframes:
res = BlastCLI.s2s_blast(cds, frame, self.evalue, command='blastp', task='blastp')
if res: results.extend(res)
hsps = BlastCLI.all_hsps(results)
if not hsps: return [(None, None, None)]
f1 = []
f2 = []
col = []
fname = self._feature_name(f, default='CDS')
cds_len = len(cds)
min_len = len(cds) * self.min_length
for hsp in hsps:
if hsp.align_length < min_len: continue
if hsp.identities / float(hsp.align_length) < self.min_identity: continue
color_t = (float(hsp.identities) / hsp.align_length)
print '%s %s: %5.1f%% (%5.1f%%)' % (c1.description, fname, color_t * 100, float(hsp.identities) / cds_len * 100)
col.append(colors.linearlyInterpolatedColor(colors.Color(0, 0, 1, 0.2), colors.Color(0, 1, 0, 0.2),
0.2, 1, color_t))
qstart = (hsp.query_start - 1) * 3
qend = qstart + hsp.align_length * 3
sstart = (hsp.sbjct_start - 1) * 3
send = sstart + hsp.align_length * 3
f1.append(
SeqFeature(FeatureLocation(f.location.start + qstart, f.location.start + qend, strand=hsp.strand[0])))
f2.append(SeqFeature(FeatureLocation(sstart, send, strand=hsp.strand[1])))
return zip(f1, f2, col)
def _blast_feature(self, f, c1, c2, features1, features2, evalue,
max_rlen):
trans = Translator(self._abort_event)
cds = trans.translate(f.extract(c1), 11)
sixframes = trans.translate_six_frames_single(c2, 11)
if not sixframes: return [(None, None, None)]
results = []
for frame in sixframes:
res = BlastCLI.s2s_blast(cds,
frame,
evalue,
command='blastp',
task='blastp')
if res: results.extend(res)
hsps = BlastCLI.all_hsps(results, max_rlen)
if not hsps: return [(None, None, None)]
f1 = []
f2 = []
col = []
c1_name = pretty_rec_name(c1)
if 'locus_tag' in f.qualifiers:
fname = f.qualifiers['locus_tag'][0]
else:
fname = 'CDS'
cds_len = len(cds)
for hsp in hsps:
color_t = (float(hsp.identities) / hsp.align_length)
print '%s %s: %5.1f%% (%5.1f%%)' % (c1_name, fname, color_t * 100,
float(hsp.identities) /
cds_len * 100)
col.append(
colors.linearlyInterpolatedColor(colors.Color(0, 0, 1, 0.2),
colors.Color(0, 1, 0, 0.2),
0.2, 1, color_t))
qstart = (hsp.query_start - 1) * 3
qend = qstart + hsp.align_length * 3
sstart = (hsp.sbjct_start - 1) * 3
send = sstart + hsp.align_length * 3
f1.append(
SeqFeature(
FeatureLocation(f.location.start + qstart,
f.location.start + qend,
strand=hsp.strand[0])))
f2.append(
SeqFeature(FeatureLocation(sstart, send,
strand=hsp.strand[1])))
return zip(f1, f2, col)