def hmmbuild(alignment, outfile, name=None, **kwargs):
unlink_file = False
if isinstance(alignment, str): msafile = alignment
elif isinstance(alignment, MultipleSeqAlignment):
msafile = AlignmentUtils.mktmp(alignment)
if not msafile: return False
unlink_file = True
else:
print 'Alignment must be either a filename or an instance of MultipleSeqAlignment'
return False
if not name: name = FilenameParser.strip_ext(os.path.basename(outfile))
ret = run_cline(HMMBuildCommandline(input=msafile,
out=outfile,
n=name,
cpu=cpu_count,
seed=0,
**kwargs),
_msg='Unable to build HMM profile')
if unlink_file: os.unlink(msafile)
return ret
def hmmbuild(alignment, outfile, name=None, **kwargs):
msafile = AlignmentUtils.mktmp(alignment)
if not name: name = FilenameParser.strip_ext(outfile)
return run_cline(HMMBuildCommandline(input=msafile, out=outfile,
n=name, cpu=cpu_count, seed=0, **kwargs),
_msg = 'Unable to build HMM profile')
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):
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'