def blast_genes(self, db, evalue=10, **kwargs):
gresults = [None] * len(self)
for g in self.genes:
s = g.extract(self.contig)
results = BlastCLI.blast_seq(s, db, evalue, **kwargs)
print
print 'Results: %s' % str(results)
if not results:
print 'No results'
continue
print g
for rec in results:
print 'Record: %s, %d alignments' % (str(rec),
len(rec.alignments))
for alignment in rec.alignments:
print 'Alignment: %s' % alignment
for hsp in alignment.hsps:
print 'HSP: %s' % hsp
def _main(self):
email = '*****@*****.**'
genome_dir = '/home/allis/Dropbox/Science/Микра/Thermococcus/sequence/GenBank/Thermococcales/Thermococcus/'
genome = 'Thermococcus_barophilus_Ch5.gb'
gene = 'TBCH5v1_1369' #cooS
database = 'nr'
segment = [3200, 12000]
seq = SeqLoader.load_file(os.path.join(genome_dir, genome))
if not seq: raise RuntimeError('No genome loaded')
seq = seq[0]
index = get_indexes_of_genes(seq, gene)
if not index: raise RuntimeError('No gene found')
feature = seq.features[index[0]]
query = feature.extract(seq)
segments_file = 'CO-clusters.gb'
#get cluster variants if needed
if not os.path.isfile(segments_file):
blast_file = 'blast.results.xml'
if os.path.isfile(blast_file):
blast = list(parse(open(blast_file)))
else:
blast = BlastCLI.blast_seq(query,
database,
100,
remote=True,
task='blastn',
parse_results=True,
save_results_to='blast.results.xml')
if not blast: raise RuntimeError('Blast returned no results')
flt = BlastFilter(lambda hsp, r: hsp.align_length > 700,
filter_hsps=True)
flt(blast)
queries = []
for ali in BlastCLI.iter_alignments(blast):
q = BlastCLI.Query(ali,
'hsp',
start_offset=segment[0],
end_offset=segment[1])
if q: queries.append(q)
print(queries[-1])
segments = BlastWWW.fetch_queries(email, queries)
safe_write(segments, segments_file)
for r in segments:
print('[%s] %s: %dbp' % (r.id, pretty_rec_name(r), len(r)))
return 0
#find primers in alignments of the selected features
local_files = [
os.path.join(genome_dir, f)
for f in ('Thermococcus_barophilus_DT4-complete-genome.gb',
'Thermococcus_ST-423.gb', 'Thermococcus_CH1-complete.gb')
]
loader = SeqLoader(self.abort_event)
segments = loader.load_files([segments_file] + local_files)
fprimers, transF_ali = find_primers(
segments, 'transF',
dict(plen=(20, 30),
max_mismatches=5,
min_first_matches=3,
AT_first=True))
rprimers, cooS_ali = find_primers(segments,
'cooS',
dict(plen=(20, 30),
max_mismatches=4,
min_first_matches=3,
AT_first=True),
reverse=True)
if not fprimers:
print('\nNo forward primers found')
return 1
if not rprimers:
print('\nNo reverse primers found')
return 1
print('\nForward primers:')
for p in fprimers:
print('%s: %s' % (p.id, p))
print('\nReverse primers:')
for p in rprimers:
print('%s: %s' % (p.id, p))
print()
#add primers to alignments and save them
transF_ali = PrimerFinder.add_primers_to_alignment(
fprimers, transF_ali)
cooS_ali = PrimerFinder.add_primers_to_alignment(rprimers,
cooS_ali,
reverse=True)
AlignmentUtils.save(transF_ali, 'transF.aln')
AlignmentUtils.save(cooS_ali, 'cooS.aln')
