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refsel - permit failure of scaffolding to some references as long as …
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…at least one scaffolding succeeds
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@notestaff
notestaff committed Dec 14, 2017
1 parent 596028e commit 8723ef4
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Showing 5 changed files with 200 additions and 16 deletions.
18 changes: 10 additions & 8 deletions assembly.py
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Expand Up @@ -519,26 +519,28 @@ def order_and_orient(inFasta, inReference, outFasta,

n_refs = len(ref_segments_all) // n_genome_segments
log.info('n_genome_segments={} n_refs={}'.format(n_genome_segments, n_refs))
ref_ids = []

with util.file.tempfnames(suffixes=[ '.{}.ref.fasta'.format(ref_num) for ref_num in range(n_refs)]) as refs_fasta, \
util.file.tempfnames(suffixes=[ '.{}.scaffold.fasta'.format(ref_num) for ref_num in range(n_refs)]) as scaffolds_fasta, \
util.file.tempfnames(suffixes=[ '.{}.altcontig.fasta'.format(ref_num) for ref_num in range(n_refs)]) as alt_contigs_fasta:

for ref_num in range(n_refs):
Bio.SeqIO.write(ref_segments_all[ref_num*n_genome_segments : (ref_num+1)*n_genome_segments], refs_fasta[ref_num], 'fasta')
this_ref_segs = ref_segments_all[ref_num*n_genome_segments : (ref_num+1)*n_genome_segments]
ref_ids.append(this_ref_segs[0].id)
Bio.SeqIO.write(this_ref_segs, refs_fasta[ref_num], 'fasta')

with concurrent.futures.ProcessPoolExecutor(max_workers=util.misc.sanitize_thread_count(threads)) as executor:
executor.map(functools.partial(_call_order_and_orient_orig, inFasta=inFasta,
breaklen=breaklen, maxgap=maxgap, minmatch=minmatch, mincluster=mincluster, min_pct_id=min_pct_id,
min_contig_len=min_contig_len, min_pct_contig_aligned=min_pct_contig_aligned),
refs_fasta, scaffolds_fasta, alt_contigs_fasta)

refs = [tuple(Bio.SeqIO.parse(scaffolds_fasta[ref_num], 'fasta')) for ref_num in range(n_refs)]
assert set(map(len, refs))==set([n_genome_segments]), \
'Some computed scaffold does not have the number of segments that the reference genome has ({}): {})'.format(n_genome_segments, map(len,refs))

base_counts = [sum([len(rec.seq.ungap('N')) for rec in ref]) for ref in refs]
scaffolds = [tuple(Bio.SeqIO.parse(scaffolds_fasta[ref_num], 'fasta')) for ref_num in range(n_refs)]
base_counts = [sum([len(seg.seq.ungap('N')) for seg in scaffold]) \
if len(scaffold)==n_genome_segments else 0 for scaffold in scaffolds]
best_ref_num = numpy.argmax(base_counts)
assert len(scaffolds[best_ref_num])==n_genome_segments, 'All computed scaffolds are incomplete'
log.info('base_counts={} best_ref_num={}'.format(base_counts, best_ref_num))
shutil.copyfile(scaffolds_fasta[best_ref_num], outFasta)
if outAlternateContigs:
Expand All @@ -550,8 +552,8 @@ def order_and_orient(inFasta, inReference, outFasta,
with open(outStats, 'w') as stats_f:
stats_w = csv.DictWriter(stats_f, fieldnames='ref_num ref_name base_count rank'.split(), delimiter='\t')
stats_w.writeheader()
for ref_num, (ref, base_count, rank) in enumerate(zip(refs, base_counts, ref_ranks)):
stats_w.writerow({'ref_num': ref_num, 'ref_name': ref[0].id, 'base_count': base_count, 'rank': rank})
for ref_num, (ref_id, base_count, rank) in enumerate(zip(ref_ids, base_counts, ref_ranks)):
stats_w.writerow({'ref_num': ref_num, 'ref_name': ref_id, 'base_count': base_count, 'rank': rank})


def parser_order_and_orient(parser=argparse.ArgumentParser()):
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6 changes: 3 additions & 3 deletions test/input/TestOrderAndOrient/expected.refsel.ebov.stats.tsv
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@@ -1,4 +1,4 @@
ref_num ref_name base_count rank
0 KX009902.1_contigs_ordered_and_oriented 18502 1
1 KM034550.1_contigs_ordered_and_oriented 18572 0
2 KT765130.1_contigs_ordered_and_oriented 18485 2
0 KX009902.1 18502 1
1 KM034550.1 18572 0
2 KT765130.1 18485 2
9 changes: 5 additions & 4 deletions test/input/TestOrderAndOrient/expected.refsel.lasv.stats.tsv
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@@ -1,5 +1,6 @@
ref_num ref_name base_count rank
0 gi|23343509|ref|NC_004296.1|_contigs_ordered_and_oriented 10671 0
1 gi|695316025|gb|KM822128.1|_contigs_ordered_and_oriented 6192 3
2 LASV-G502-S-Sierra_Leone-2009H_contigs_ordered_and_oriented 10655 1
3 GU481072_contigs_ordered_and_oriented 9213 2
0 gi|23343509|ref|NC_004296.1| 10671 0
1 gi|695316025|gb|KM822128.1| 6192 3
2 LASV-G502-S-Sierra_Leone-2009H 10655 1
3 GU481072 9213 2
4 nomatch.1|LASV-sized-blank-S 0 4
181 changes: 181 additions & 0 deletions test/input/TestOrderAndOrient/ref.lasv.nomatch.fasta
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>nomatch.2|LASV-sized-blank-L
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2 changes: 1 addition & 1 deletion test/unit/test_assembly.py
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Expand Up @@ -278,7 +278,7 @@ def test_lassa_multisegment_refsel(self):
'expected.lasv.fasta',
'expected.refsel.lasv.stats.tsv')
refs = [self.input('ref.lasv.{}.fasta'.format(strain))
for strain in ('josiah', 'pinneo', 'KGH_G502', 'BNI_Nig08_A19')]
for strain in ('josiah', 'pinneo', 'KGH_G502', 'BNI_Nig08_A19', 'nomatch')]
assembly.order_and_orient(contigs, refs, outFasta,
outReference=outReference, outStats=outStats)
self.assertEqualContents(outFasta, expected)
Expand Down

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