def get_subtype_reference_alignment_consensus(region,
subtype='B',
refname='HXB2',
type='nuc',
VERBOSE=0):
'''Get filename of consensus of subtype reference alignment'''
from Bio import SeqIO
from hivwholeseq.cross_sectional.filenames import (
get_subtype_reference_alignment_consensus_filename)
fn = get_subtype_reference_alignment_consensus_filename(region,
subtype=subtype,
refname=refname,
type=type,
VERBOSE=VERBOSE)
return SeqIO.read(fn, 'fasta')
def get_subtype_reference_alignment_consensus(region,
subtype='B',
refname='HXB2',
type='nuc',
VERBOSE=0):
'''Get filename of consensus of subtype reference alignment'''
from Bio import SeqIO
from hivwholeseq.cross_sectional.filenames import (
get_subtype_reference_alignment_consensus_filename)
fn = get_subtype_reference_alignment_consensus_filename(region,
subtype=subtype,
refname=refname,
type=type,
VERBOSE=VERBOSE)
return SeqIO.read(fn, 'fasta')
VERBOSE=VERBOSE)
afs = np.load(fn_in)
if VERBOSE >= 2:
print 'Calculate consensus'
consm = alphabet[afs[:5].argmax(axis=0)]
consrec = SeqRecord(Seq(''.join(consm), alphabet_bio),
id='consensus_subtype'+subtype+'_refto_'+refname,
name='consensus_subtype'+subtype+'_refto_'+refname,
description=('Consensus of subtype '+subtype+
' reference alignment to '+refname),
)
if VERBOSE >= 2:
print 'Save to file'
fn_out = get_subtype_reference_alignment_consensus_filename(region,
subtype=subtype,
refname=refname,
type=alitype,
VERBOSE=VERBOSE)
SeqIO.write(consrec, fn_out, 'fasta')
else:
consrec = get_subtype_reference_alignment_consensus(region,
subtype=subtype,
refname=refname,
type=alitype,
VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Calculate consensus'
consm = alphabet[afs[:5].argmax(axis=0)]
consrec = SeqRecord(
Seq(''.join(consm), alphabet_bio),
id='consensus_subtype' + subtype + '_refto_' + refname,
name='consensus_subtype' + subtype + '_refto_' + refname,
description=('Consensus of subtype ' + subtype +
' reference alignment to ' + refname),
)
if VERBOSE >= 2:
print 'Save to file'
fn_out = get_subtype_reference_alignment_consensus_filename(
region,
subtype=subtype,
refname=refname,
type=alitype,
VERBOSE=VERBOSE)
SeqIO.write(consrec, fn_out, 'fasta')
else:
consrec = get_subtype_reference_alignment_consensus(
region,
subtype=subtype,
refname=refname,
type=alitype,
VERBOSE=VERBOSE)
