def get_map_overlap(sample, fr1, fr2):
'''Get a coordinate map of the overlap between the two fragments'''
import numpy as np
from seqanpy import align_ladder
seq1 = sample.get_reference(fr1)
seq2 = sample.get_reference(fr2)
(score, ali1, ali2) = align_ladder(seq1, seq2, score_gapopen=-20)
start2 = len(ali2) - len(ali2.lstrip('-'))
end1 = len(ali1.rstrip('-'))
mapco = []
pos1 = start2
pos2 = 0
for i in xrange(start2, end1):
if (ali1[i] != '-') and (ali2[i] != '-'):
mapco.append((pos1, pos2))
if ali1[i] != '-':
pos1 += 1
if ali2[i] != '-':
pos2 += 1
return np.array(mapco, int)
def join_block_to_consensus(consensus, cons_block, VERBOSE=0, deltamax=60):
'''Join a new block to an extant consensus'''
import numpy as np
from seqanpy import align_ladder
(score, ali1, ali2) = align_ladder(consensus, cons_block, score_gapopen=-10)
if VERBOSE >= 3:
from hivwholeseq.utils.sequence import pretty_print_pairwise_ali
pretty_print_pairwise_ali([ali1, ali2], name1='consensus', name2='new block')
# In very rare occasions (coverage holes), the second sequence is actually
# shorter than the first, then we do not need to glue it in
if ali2[-1] == '-':
if VERBOSE >= 2:
print 'WARNING: the old block is longer than the new one (maybe low coverage)'
return consensus
end1 = len(ali1.rstrip('-'))
start2 = len(ali2) - len(ali2.lstrip('-'))
scoremax = 3 * (end1 - start2)
delta = scoremax - score
if delta > deltamax:
raise ValueError('Too many mismatches in neighbouring local consensi! ('+str(delta)+', max '+str(deltamax)+')')
consensus = (ali1[:start2] + ali2[start2:]).replace('-', '')
return consensus
def align_fragments(c1, c2, VERBOSE=0):
'''Align subsequence fragments'''
import numpy as np
from seqanpy import align_ladder
from hivwholeseq.utils.sequence import pretty_print_pairwise_ali
(score, a1, a2) = align_ladder(c1, c2, score_gapopen=-20)
start2 = len(a2) - len(a2.lstrip('-'))
end1 = len(a1.rstrip('-'))
a1 = a1[start2: end1]
a2 = a2[start2: end1]
if VERBOSE >= 3:
pretty_print_pairwise_ali((a1, a2), width=100,
name1=fr1, name2=fr2)
a1 = np.fromstring(a1, 'S1')
a2 = np.fromstring(a2, 'S1')
co1 = (a1 != '-').cumsum() - 1
co2 = (a2 != '-').cumsum() - 1
ind = (a1 != '-') & (a2 != '-')
pos1 = co1[ind] + start2
pos2 = co2[ind]
return (pos1, pos2)
def get_map_overlap(sample, fr1, fr2):
'''Get a coordinate map of the overlap between the two fragments'''
import numpy as np
from seqanpy import align_ladder
seq1 = sample.get_reference(fr1)
seq2 = sample.get_reference(fr2)
(score, ali1, ali2) = align_ladder(seq1, seq2, score_gapopen=-20)
start2 = len(ali2) - len(ali2.lstrip('-'))
end1 = len(ali1.rstrip('-'))
mapco = []
pos1 = start2
pos2 = 0
for i in xrange(start2, end1):
if (ali1[i] != '-') and (ali2[i] != '-'):
mapco.append((pos1, pos2))
if ali1[i] != '-':
pos1 += 1
if ali2[i] != '-':
pos2 += 1
return np.array(mapco, int)
def join_block_to_consensus(consensus, cons_block, VERBOSE=0, deltamax=60):
'''Join a new block to an extant consensus'''
import numpy as np
from seqanpy import align_ladder
(score, ali1, ali2) = align_ladder(consensus,
cons_block,
score_gapopen=-10)
if VERBOSE >= 3:
from hivwholeseq.utils.sequence import pretty_print_pairwise_ali
pretty_print_pairwise_ali([ali1, ali2],
name1='consensus',
name2='new block')
# In very rare occasions (coverage holes), the second sequence is actually
# shorter than the first, then we do not need to glue it in
if ali2[-1] == '-':
if VERBOSE >= 2:
print 'WARNING: the old block is longer than the new one (maybe low coverage)'
return consensus
end1 = len(ali1.rstrip('-'))
start2 = len(ali2) - len(ali2.lstrip('-'))
scoremax = 3 * (end1 - start2)
delta = scoremax - score
if delta > deltamax:
raise ValueError(
'Too many mismatches in neighbouring local consensi! (' +
str(delta) + ', max ' + str(deltamax) + ')')
consensus = (ali1[:start2] + ali2[start2:]).replace('-', '')
return consensus
def merge_sequences(seqs, skip_initial=30, accept_gaps=False, VERBOSE=0):
'''Merge sequences with overlaps
Parameters:
seqs (list): sequences to merge
skip_initial (int): trim from the beginning of overlaps because we do not
really trust those bases
accept_gaps (bool): accept gaps in the overlaps
'''
from itertools import izip
from seqanpy import align_ladder
import numpy as np
seqs = map(''.join, seqs)
left_trim = 0
seqs_all = []
for iov, (seq1, seq2) in enumerate(izip(seqs[:-1], seqs[1:])):
if VERBOSE >= 1:
print 'Overlap n', iov+1
(score, ali1, ali2) = align_ladder(seq1[left_trim:], seq2, score_gapopen=-20)
start2 = len(ali2) - len(ali2.lstrip('-'))
end1 = len(ali1.rstrip('-'))
# Append first sequence until overlap
seqs_all.append(ali1[:start2 + skip_initial])
# Check overlap
ov1 = ali1[start2 + skip_initial: end1 - skip_initial]
ov2 = ali2[start2 + skip_initial: end1 - skip_initial]
if VERBOSE >= 2:
from hivwholeseq.utils.sequence import pretty_print_pairwise_ali
pretty_print_pairwise_ali((ov1, ov2), width=100,
name1='seq1', name2='seq2')
if (not accept_gaps) and (('-' in ov1) or ('-' in ov2)):
raise ValueError('Gaps in the overlap n. '+str(iov+1))
# Trust the first sequence until half, then the other one
i_mid = len(ov1) // 2
seqs_all.append(ov1[:i_mid])
seqs_all.append(ov2[i_mid:])
# Set the left trim for the trailing sequence
left_trim = len(ali2[: end1 - skip_initial].replace('-', ''))
if VERBOSE >= 1:
print 'Add last sequence'
seqs_all.append(seq2[left_trim:])
return ''.join(seqs_all)
def merge_read_pair(seq1, seq2):
'''Merge two reads of a pair, assuming the second starts later'''
from seqanpy import align_ladder
(score, ali1, ali2) = align_ladder(seq1, seq2, score_gapopen=-20)
end1 = len(ali1.rstrip('-'))
start2 = len(ali2) - len(ali2.lstrip('-'))
overlap_ali = np.vstack([np.fromstring(a[start2: end1], 'S1')
for a in (ali1, ali2)])
overlap = overlap_ali[0]
overlap[overlap_ali[0] != overlap_ali[1]] = 'N'
overlap = overlap.tostring()
seq = ali1[:start2] + overlap + ali2[end1:]
return seq
def merge_read_pair(seq1, seq2):
'''Merge two reads of a pair, assuming the second starts later'''
from seqanpy import align_ladder
(score, ali1, ali2) = align_ladder(seq1, seq2, score_gapopen=-20)
end1 = len(ali1.rstrip('-'))
start2 = len(ali2) - len(ali2.lstrip('-'))
overlap_ali = np.vstack(
[np.fromstring(a[start2:end1], 'S1') for a in (ali1, ali2)])
overlap = overlap_ali[0]
overlap[overlap_ali[0] != overlap_ali[1]] = 'N'
overlap = overlap.tostring()
seq = ali1[:start2] + overlap + ali2[end1:]
return seq
def check_reference_overlap(p, VERBOSE=0):
'''Check whether the reference from the various fragments overlap correctly'''
from seqanpy import align_ladder
from hivwholeseq.utils.sequence import pretty_print_pairwise_ali
fragments = ['F' + str(i + 1) for i in xrange(6)]
title = 'Overlaps'
line = ('{:<' + str(title_len) + '}').format(title + ':')
stati = []
for i in xrange(len(fragments) - 1):
ref1 = p.get_reference(fragments[i])
ref2 = p.get_reference(fragments[i + 1])
(score, ali1, ali2) = align_ladder(ref1,
ref2,
score_gapopen=-10,
score_gapext=-1)
start2 = len(ali2) - len(ali2.lstrip('-'))
end1 = len(ali1.rstrip('-'))
if VERBOSE >= 4:
pretty_print_pairwise_ali((ali1[start2:end1], ali2[start2:end1]),
name1=fragments[i],
name2=fragments[i + 1],
width=100)
if ali1[start2:end1].count('-') == ali2[start2:end1].count('-'):
status = 'OK'
else:
status = 'GAPS'
import ipdb
ipdb.set_trace()
line = line+fragments[i]+': '+\
('{:>'+str(cell_len - len(fragments[i]) - 1)+'}').format(status)+' '
stati.append(status)
print line
if 'GAPS' in stati:
raise ValueError('GAPS status found')
def check_reference_overlap(p, VERBOSE=0):
'''Check whether the reference from the various fragments overlap correctly'''
from seqanpy import align_ladder
from hivwholeseq.utils.sequence import pretty_print_pairwise_ali
fragments = ['F'+str(i+1) for i in xrange(6)]
title = 'Overlaps'
line = ('{:<'+str(title_len)+'}').format(title+':')
stati = []
for i in xrange(len(fragments) - 1):
ref1 = p.get_reference(fragments[i])
ref2 = p.get_reference(fragments[i+1])
(score, ali1, ali2) = align_ladder(ref1, ref2,
score_gapopen=-10,
score_gapext=-1)
start2 = len(ali2) - len(ali2.lstrip('-'))
end1 = len(ali1.rstrip('-'))
if VERBOSE >= 4:
pretty_print_pairwise_ali((ali1[start2: end1], ali2[start2: end1]),
name1=fragments[i],
name2=fragments[i+1],
width=100)
if ali1[start2: end1].count('-') == ali2[start2: end1].count('-'):
status = 'OK'
else:
status = 'GAPS'
import ipdb; ipdb.set_trace()
line = line+fragments[i]+': '+\
('{:>'+str(cell_len - len(fragments[i]) - 1)+'}').format(status)+' '
stati.append(status)
print line
if 'GAPS' in stati:
raise ValueError('GAPS status found')
def merge_sequences_fragments(seqs, VERBOSE=0):
'''Merge sequences from consecutive fragments'''
from seqanpy import align_ladder
seqs = map(''.join, seqs)
seq = [seqs[0]]
for seq2 in seqs[1:]:
seq1 = seq[-1]
(score, ali1, ali2) = align_ladder(seq1, seq2, score_gapopen=-20)
start2 = len(ali2) - len(ali2.lstrip('-'))
end1 = len(ali1.rstrip('-'))
len_overlap = end1 - start2
# Trust the first sequence in the first half, the second in the second
overlap = ali1[start2: start2 + len_overlap / 2] + \
ali2[start2 + len_overlap / 2: end1]
seq[-1] = ali1[:start2]
seq.append(overlap)
seq.append(ali2[end1:])
seq = ''.join(seq)
return seq
def merge_fragments(sequences, name='', VERBOSE=0):
'''Merge references at overlapping pairs'''
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import ambiguous_dna
from seqanpy import align_ladder
from hivwholeseq.utils.sequence import pretty_print_pairwise_ali
consensus = []
seq_old = ''.join(sequences['F1'])
for i in xrange(5):
seq_new = ''.join(sequences['F'+str(i+2)])
(score, ali1, ali2) = align_ladder(seq_old, seq_new, score_gapopen=-10)
if VERBOSE >= 3:
pretty_print_pairwise_ali([ali1, ali2], name1='F'+str(i+1), name2='F'+str(i+2))
# Overlap: the first sequence is better at the start, the second at the end
end1 = len(ali1.rstrip('-'))
start2 = len(ali2) - len(ali2.lstrip('-'))
len_overlap = end1 - start2
# There might a too short consensus, just join them with N
if len_overlap < 50:
consensus.append(seq_old)
consensus.append('N' * 10)
if i == 4:
consensus.append(seq_new)
else:
seq_old = seq_new
continue
overlap1 = np.fromstring(ali1[start2: end1], 'S1')
overlap2 = np.fromstring(ali2[start2: end1], 'S1')
overlap = overlap1.copy()
ind_overlap_mismatch = (overlap1 != overlap2).nonzero()[0]
for j in ind_overlap_mismatch:
if j < len(overlap) // 3:
continue
elif j < 2 * len(overlap) // 3:
overlap[j] = 'N'
else:
overlap[j] = overlap2[j]
overlap = overlap.tostring()
consensus.append(ali1[:start2])
consensus.append(overlap)
if i == 4:
consensus.append(ali2[end1:])
else:
seq_old = ali2[end1:].replace('-', '')
consensus = ''.join(consensus)
cons_rec = SeqRecord(Seq(consensus, IUPAC.ambiguous_dna),
id=name, name=name,
description=name+', genomewide')
return cons_rec
# Global pairwise alignment
seq1 = 'AAAGGTCTA'
seq2 = 'AAATCGA'
output = sap.align_global(seq1, seq2, band=5)
print output
# Overlap pairwise alignment
seq1 = 'AAAGGTCTA'
seq2 = 'ATCT'
output = sap.align_overlap(seq1, seq2)
print output
# Overlap pairwise alignment cutting flanks
seq1 = 'AAAGGTCTA'
seq2 = 'ATCT'
output = sap.align_overlap(seq1, seq2, cut_flanks=True)
print output
# Ladder pairwise alignment
seq1 = 'AAAGGTCTA'
seq2 = 'TCTAGGGAAACCC'
output = sap.align_ladder(seq1, seq2)
print output
# Local pairwise alignment
seq1 = 'AAAGGTCTACCGTAGCCT'
seq2 = 'AAGTCTAC'
output = sap.align_local(seq1, seq2)
print output
def merge_fragments(sequences, name='', VERBOSE=0):
'''Merge references at overlapping pairs'''
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import ambiguous_dna
from seqanpy import align_ladder
from hivwholeseq.utils.sequence import pretty_print_pairwise_ali
consensus = []
seq_old = ''.join(sequences['F1'])
for i in xrange(5):
seq_new = ''.join(sequences['F' + str(i + 2)])
(score, ali1, ali2) = align_ladder(seq_old, seq_new, score_gapopen=-10)
if VERBOSE >= 3:
pretty_print_pairwise_ali([ali1, ali2],
name1='F' + str(i + 1),
name2='F' + str(i + 2))
# Overlap: the first sequence is better at the start, the second at the end
end1 = len(ali1.rstrip('-'))
start2 = len(ali2) - len(ali2.lstrip('-'))
len_overlap = end1 - start2
# There might a too short consensus, just join them with N
if len_overlap < 50:
consensus.append(seq_old)
consensus.append('N' * 10)
if i == 4:
consensus.append(seq_new)
else:
seq_old = seq_new
continue
overlap1 = np.fromstring(ali1[start2:end1], 'S1')
overlap2 = np.fromstring(ali2[start2:end1], 'S1')
overlap = overlap1.copy()
ind_overlap_mismatch = (overlap1 != overlap2).nonzero()[0]
for j in ind_overlap_mismatch:
if j < len(overlap) // 3:
continue
elif j < 2 * len(overlap) // 3:
overlap[j] = 'N'
else:
overlap[j] = overlap2[j]
overlap = overlap.tostring()
consensus.append(ali1[:start2])
consensus.append(overlap)
if i == 4:
consensus.append(ali2[end1:])
else:
seq_old = ali2[end1:].replace('-', '')
consensus = ''.join(consensus)
cons_rec = SeqRecord(Seq(consensus, IUPAC.ambiguous_dna),
id=name,
name=name,
description=name + ', genomewide')
return cons_rec
def overlap_ladder():
print('Test align_ladder')
import seqanpy
(score, ali1, ali2) = seqanpy.align_ladder('ACCGT', 'CGTAA')
assert ali1 == 'ACCGT--'
assert ali2 == '--CGTAA'
