def _main(self):
min_prod = 400
silva_db = '/home/allis/Documents/INMI/SILVA-DB/SILVA_123_SSURef_Nr99_tax_silva.fasta'
alifile = '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.aln.fasta'
add_filename = FilenameParser.strip_ext(
alifile) + '.with_additions.fasta'
outgroups = [
'Thermococcus_chitonophagus', 'SMTZ1-55',
'contig72135_1581_sunspring_meta'
]
add = ['KF836721.1.1270', 'EU635905.1.1323']
exclude = [
] #['Thermococcus_chitonophagus', 'SMTZ1-55', 'BA1-16S', 'contig72135_1581_sunspring_meta']
#load alignment
if os.path.isfile(add_filename):
alifile = add_filename
add_filename = ''
with user_message('Loadding initial alignment...', '\n'):
orig_ali = AlignmentUtils.load_first(alifile)
if not orig_ali: return 1
#load homologs
if add_filename:
with user_message('Loadding additional sequences...', '\n'):
add_seqs = []
db = SeqView()
if db.load(silva_db):
for sid in add:
seq = db.get(sid)
if seq: add_seqs.append(seq)
else: print '%s not found in %s' % (sid, silva_db)
#realign data if needed
if add_seqs:
with user_message('Realigning data...', '\n'):
add_filename = FilenameParser.strip_ext(
alifile) + '.with_additions.fasta'
AlignmentUtils.align(
list(orig_ali) + add_seqs, add_filename)
orig_ali = AlignmentUtils.load_first(add_filename)
if not orig_ali: return 2
#process the alignment
ali = orig_ali.remove(*exclude).trim()
for out in outgroups:
if not ali.index(out):
print '%s not found in the alignment' % out
return 3
ali.sort(key=lambda r: 'zzzzzzzz' if r.id in outgroups else r.id)
AlignmentUtils.save(
ali,
'/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.aln.trimmed.fasta'
)
args = dict(plen=(20, 40),
max_mismatches=8,
min_match_mismatches=1,
first_match_mismatches=1,
first_may_match=1,
AT_first=True,
outgroup=len(outgroups))
fprimers = PrimerFinder.find_discriminating_primers(ali, **args)
rprimers = PrimerFinder.find_discriminating_primers(ali,
reverse=True,
**args)
pairs = PrimerFinder.compile_pairs(fprimers, rprimers, min_prod,
'SSBa')
if not pairs:
print '\nNo suitable primer pairs found'
return 3
PrimerFinder.print_pairs(pairs)
orig_ali = PrimerFinder.add_pairs_to_alignment(pairs, orig_ali)
AlignmentUtils.save(
orig_ali,
'/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.with_primers.aln.fasta'
)
print 'Done'
def _main(self):
min_prod = 400
silva_db = '/home/allis/Documents/INMI/SILVA-DB/SILVA_123_SSURef_Nr99_tax_silva.fasta'
alifile = '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.aln.fasta'
add_filename = FilenameParser.strip_ext(alifile)+'.with_additions.fasta'
outgroups = ['Thermococcus_chitonophagus', 'SMTZ1-55', 'contig72135_1581_sunspring_meta']
add = ['KF836721.1.1270','EU635905.1.1323']
exclude = []#['Thermococcus_chitonophagus', 'SMTZ1-55', 'BA1-16S', 'contig72135_1581_sunspring_meta']
#load alignment
if os.path.isfile(add_filename):
alifile = add_filename
add_filename = ''
with user_message('Loadding initial alignment...', '\n'):
orig_ali = AlignmentUtils.load_first(alifile)
if not orig_ali: return 1
#load homologs
if add_filename:
with user_message('Loadding additional sequences...', '\n'):
add_seqs = []
db = SeqView()
if db.load(silva_db):
for sid in add:
seq = db.get(sid)
if seq: add_seqs.append(seq)
else: print '%s not found in %s' % (sid, silva_db)
#realign data if needed
if add_seqs:
with user_message('Realigning data...', '\n'):
add_filename = FilenameParser.strip_ext(alifile)+'.with_additions.fasta'
AlignmentUtils.align(list(orig_ali)+add_seqs, add_filename)
orig_ali = AlignmentUtils.load_first(add_filename)
if not orig_ali: return 2
#process the alignment
ali = orig_ali.remove(*exclude).trim()
for out in outgroups:
if not ali.index(out):
print '%s not found in the alignment' % out
return 3
ali.sort(key=lambda r: 'zzzzzzzz' if r.id in outgroups else r.id)
ali_len = ali.get_alignment_length()
AlignmentUtils.save(ali, '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.aln.trimmed.fasta')
args = dict(plen = (20,40),
max_mismatches = 8,
min_match_mismatches = 1,
first_match_mismatches = 1,
first_may_match = 1,
AT_first=True,
outgroup=len(outgroups))
fprimers = self._find_primers(ali, **args)
rprimers = self._find_primers(ali.reverse_complement(), **args)
pairs = []
for i, (fs, fp) in enumerate(fprimers):
start = fs
fprimer = Primer.from_sequences(fp[:-1], 1, 'SSBaF%d' % fs)
for _j, (rs, rp) in enumerate(rprimers):
end = ali_len-rs
if end-start <= min_prod: continue
pairs.append((fprimer, Primer.from_sequences(rp[:-1], 1, 'SSBaR%d' % (ali_len-rs+1))))
if not pairs:
print '\nNo suitable primer pairs found'
return 3
added = set()
for i, (fp, rp) in enumerate(pairs):
print '\npair %d' % (i+1)
print '%s: %s' % (fp.id, fp)
print '%s: %s' % (rp.id, rp)
if fp.id not in added:
orig_ali.append(fp.master_sequence+'-'*(orig_ali.get_alignment_length()-len(fp)))
added.add(fp.id)
if rp.id not in added:
orig_ali.append(copy_attrs(rp.master_sequence,
rp.master_sequence.reverse_complement())+
'-'*(orig_ali.get_alignment_length()-len(rp)))
added.add(rp.id)
print
orig_ali = AlignmentUtils.align(orig_ali)
AlignmentUtils.save(orig_ali, '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.with_primers.aln.fasta')
print 'Done'
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')