def combine_alignments(fg_aln, bg_aln):
"""Align FG and BG to each other so column numbers match.
Uses MUSCLE for profile-profile alignment.
"""
# This would be simpler with NamedTemporaryFile, but Windows doesn't allow
# multiple open file handles on the same file, so here we are.
afd, aseqfname = tempfile.mkstemp(text=True)
os.close(afd)
bfd, bseqfname = tempfile.mkstemp(text=True)
os.close(bfd)
try:
AlignIO.write(fg_aln, aseqfname, 'fasta')
AlignIO.write(bg_aln, bseqfname, 'fasta')
output = call_quiet('muscle', '-profile', '-in1', aseqfname, '-in2',
bseqfname)
finally:
if os.path.exists(aseqfname):
os.remove(aseqfname)
if os.path.exists(bseqfname):
os.remove(bseqfname)
full_aln = AlignIO.read(StringIO(output), 'fasta')
full_aln = MultipleSeqAlignment(alnutils.remove_empty_cols(full_aln),
generic_protein)
# Save a copy
# ENH: choose a reasonable name
AlignIO.write(full_aln, '_cc_combined.seq', 'fasta')
logging.info("Wrote _cc_combined.seq")
return full_aln
def combine_alignments(fg_aln, bg_aln):
"""Align FG and BG to each other so column numbers match.
Uses MUSCLE for profile-profile alignment.
"""
# This would be simpler with NamedTemporaryFile, but Windows doesn't allow
# multiple open file handles on the same file, so here we are.
afd, aseqfname = tempfile.mkstemp(text=True)
os.close(afd)
bfd, bseqfname = tempfile.mkstemp(text=True)
os.close(bfd)
try:
AlignIO.write(fg_aln, aseqfname, 'fasta')
AlignIO.write(bg_aln, bseqfname, 'fasta')
output = subprocess.check_output([
'muscle', '-profile',
'-in1', aseqfname,
'-in2', bseqfname,
])
finally:
if os.path.exists(aseqfname):
os.remove(aseqfname)
if os.path.exists(bseqfname):
os.remove(bseqfname)
full_aln = AlignIO.read(StringIO(output), 'fasta')
full_aln = MultipleSeqAlignment(alnutils.remove_empty_cols(full_aln),
generic_protein)
# Save a copy
# ENH: choose a reasonable name
AlignIO.write(full_aln, '_cc_combined.seq', 'fasta')
logging.info("Wrote _cc_combined.seq")
return full_aln
def align_profiles(task, use_pdb=None):
"""Align several FASTA files with MAFFT. Clustal output.
Cleans: [depends].cons.seq, [target].families.fa, [target].families.seq,
[target].seq
"""
seeds, singles = [], []
# PDB alignment -- include as a seed profile if requested
subalignments, pdb_seed = task.depends[:-1], str(task.depends[-1])
if use_pdb and not is_empty(pdb_seed):
seeds.append(pdb_seed)
else:
logging.info("Empty PDB alignment: %s", pdb_seed)
# Get subfamily and subgroup consensus sequences/profiles
for subaln in subalignments:
aln = AlignIO.read(str(subaln), 'clustal')
# with open(task.target, 'w+') as outfile:
with open(ext(subaln, 'cons.seq'), 'w+') as outfile:
outfile.write(">%s consensus\n" % basename(noext(subaln)))
cons_seq = consensus.consensus(aln,
trim_ends=False,
gap_threshold=0.6)
if isdir(noext(subaln)):
# Group profiles: include the subfamily consenses, too
outfile.write(cons_seq + "\n")
for record in aln:
outfile.write(">%s\n" % record.id)
outfile.write("%s\n" % record.seq)
else:
# Ungapped family consensus sequences
outfile.write(cons_seq.replace('-', '') + "\n")
# Merge the sequences and profiles
for subconsseq in ext(subalignments, 'cons.seq'):
if isdir(subconsseq[:-9]):
# Group
seeds.append(subconsseq)
else:
singles.append(subconsseq)
# First, align/merge the single family consensus sequences
famfa = ext(task.target, 'families.fa')
allseq = ext(task.target, 'seq')
assert singles or seeds, \
'No .fasta files found to build %s' % task.target
if singles:
sh("cat %s > %s" % (' '.join(singles), famfa))
if seeds:
# Align the families with the groups
sh("mafft --quiet --amino --maxiterate 1000 %s %s > %s" %
(' '.join(['--seed ' + s for s in seeds]), famfa, allseq))
# XXX fast version
# sh("mafft --quiet --amino --auto %s %s > %s"
# % (' '.join(['--seed '+s for s in seeds]), famfa, allseq))
else:
# No group profiles -- just align the families
sh("mafft --quiet --amino --maxiterate 1000 %s > %s" % (famfa, allseq))
# Convert FASTA to "pressed" (single-row) Clustal
records = [
rec for rec in SeqIO.parse(allseq, 'fasta')
# Drop PDB-derived sequences
# if ':' not in rec.id
if 'TMalign' not in rec.description
and 'TM-score' not in rec.description and not rec.id.endswith('.pdb')
]
records = list(alnutils.remove_empty_cols(records))
if seeds:
# MAFFT prefixes seed alignments with '_seed_' -- get rid of that
for rec in records:
if rec.id.startswith('_seed_'):
rec.id = rec.id[6:]
try:
max_id_len = max(len(r.id) for r in records)
except ValueError:
# Common effup
raise ValueError("Profile alignment failed for %s.\nInputs: %s" %
(task.target, ' '.join(map(str, task.depends))))
with open(task.target, 'w+') as outfile:
outfile.write('CLUSTAL X (-like) multiple sequence alignment\n\n')
outfile.writelines([
'%s %s\n' % (rec.id.ljust(max_id_len), rec.seq) for rec in records
])
def align_structs(pdb_fnames, seed_fnames=None):
"""Align multiple PDB structures using TM-align.
Returns a list of aligned SeqRecords.
"""
# 1. Align all-v-all structure pairs with TM-align
allpairs = []
for idx, ref_pdbfn in enumerate(pdb_fnames):
assert ' ' not in ref_pdbfn
for eqv_pdbfn in pdb_fnames[idx + 1:]:
assert eqv_pdbfn != ref_pdbfn
logging.info("Aligning %s to %s", eqv_pdbfn, ref_pdbfn)
try:
tm_output = subprocess.check_output(
['TMalign', ref_pdbfn, eqv_pdbfn])
except OSError:
logging.warning("Failed command: TMalign %s %s", ref_pdbfn,
eqv_pdbfn)
for fname in (ref_pdbfn, eqv_pdbfn):
if not os.path.isfile(fname):
logging.warning("Missing file: %s", fname)
raise
#except subprocess.CalledProcessError, exc:
# raise RuntimeError("TMalign failed (returned %s):\n%s"
# % (exc.returncode, exc.output))
tm_seqpair = read_tmalign_as_seqrec_pair(tm_output, ref_pdbfn,
eqv_pdbfn)
allpairs.append(tm_seqpair)
# In case of 2 structs, no need to combine alignments -- we're done
if len(allpairs) == 1:
recs = allpairs[0][:2]
return alnutils.remove_empty_cols(recs)
# 2. Resolve MST pairs & write seed tempfiles
tmp_seed_fnames = []
allpairs_dict = {(i[0].id, i[1].id): i for i in allpairs}
for seedpairid in mst_pairs(allpairs):
seedpair = allpairs_dict[seedpairid]
# fd, seedfn = tempfile.mkstemp(text=True)
# SeqIO.write(seedpair, seedfn, 'fasta')
# SeqIO.write(seedpair, os.fdopen(fd), 'fasta')
with tempfile.NamedTemporaryFile('w+', delete=False) as handle:
SeqIO.write([seedpair[0], seedpair[1]], handle, 'fasta')
#AlignIO.write(MultipleSeqAlignment(seedpair), handle, 'fasta')
tmp_seed_fnames.append(handle.name)
# 3. Use MAFFT to combine TMalign'd pairs into a multiple alignment;
seq_fd, seq_fname = tempfile.mkstemp(text=True)
# Create a blank file to appease MAFFT
os.write(seq_fd, b'')
os.close(seq_fd)
mafft_output = subprocess.check_output([
'mafft', '--quiet', '--amino', '--localpair', '--maxiterate', '1000'
] + list(
itertools.chain(*[('--seed', sfn)
for sfn in (seed_fnames or []) + tmp_seed_fnames])) +
[seq_fname])
# Clean up
os.remove(seq_fname)
for sfn in tmp_seed_fnames:
os.remove(sfn)
# 4. Emit the aligned sequences
recs = SeqIO.parse(StringIO(mafft_output.decode("utf-8")), 'fasta')
recs = clean_and_dedupe_seqs(recs)
recs = alnutils.remove_empty_cols(recs)
recs = purge_seqs(recs)
return list(recs)
def align_profiles(task, use_pdb=None):
"""Align several FASTA files with MAFFT. Clustal output.
Cleans: [depends].cons.seq, [target].families.fa, [target].families.seq,
[target].seq
"""
seeds, singles = [], []
# PDB alignment -- include as a seed profile if requested
subalignments, pdb_seed = task.depends[:-1], str(task.depends[-1])
if use_pdb and not is_empty(pdb_seed):
seeds.append(pdb_seed)
else:
logging.info("Empty PDB alignment: %s", pdb_seed)
# Get subfamily and subgroup consensus sequences/profiles
for subaln in subalignments:
aln = AlignIO.read(str(subaln), 'clustal')
# with open(task.target, 'w+') as outfile:
with open(ext(subaln, 'cons.seq'), 'w+') as outfile:
outfile.write(">%s consensus\n" % basename(noext(subaln)))
cons_seq = consensus.consensus(aln, trim_ends=False,
gap_threshold=0.6)
if isdir(noext(subaln)):
# Group profiles: include the subfamily consenses, too
outfile.write(cons_seq + "\n")
for record in aln:
outfile.write(">%s\n" % record.id)
outfile.write("%s\n" % record.seq)
else:
# Ungapped family consensus sequences
outfile.write(cons_seq.replace('-', '') + "\n")
# Merge the sequences and profiles
for subconsseq in ext(subalignments, 'cons.seq'):
if isdir(subconsseq[:-9]):
# Group
seeds.append(subconsseq)
else:
singles.append(subconsseq)
# First, align/merge the single family consensus sequences
famfa = ext(task.target, 'families.fa')
allseq = ext(task.target, 'seq')
assert singles or seeds, \
'No .fasta files found to build %s' % task.target
if singles:
sh("cat %s > %s" % (' '.join(singles), famfa))
if seeds:
# Align the families with the groups
sh("mafft --quiet --amino --globalgenafpair --maxiterate 1000 %s %s > %s"
% (' '.join(['--seed '+s for s in seeds]), famfa, allseq))
# XXX fast version
# sh("mafft --quiet --amino --auto %s %s > %s"
# % (' '.join(['--seed '+s for s in seeds]), famfa, allseq))
else:
# No group profiles -- just align the families
sh("mafft --quiet --amino --globalgenafpair --maxiterate 1000 %s > %s"
% (famfa, allseq))
# Convert FASTA to "pressed" (single-row) Clustal
records = [rec for rec in SeqIO.parse(allseq, 'fasta')
# Drop PDB-derived sequences
# if ':' not in rec.id
if 'TMalign' not in rec.description and
'TM-score' not in rec.description and
not rec.id.endswith('.pdb')
]
records = list(alnutils.remove_empty_cols(records))
if seeds:
# MAFFT prefixes seed alignments with '_seed_' -- get rid of that
for rec in records:
if rec.id.startswith('_seed_'):
rec.id = rec.id[6:]
try:
max_id_len = max(len(r.id) for r in records)
except ValueError:
# Common effup
raise ValueError("Profile alignment failed for %s.\nInputs: %s"
% (task.target, ' '.join(map(str, task.depends))))
with open(task.target, 'w+') as outfile:
outfile.write('CLUSTAL X (-like) multiple sequence alignment\n\n')
outfile.writelines(
['%s %s\n' % (rec.id.ljust(max_id_len), rec.seq)
for rec in records])
ref_pdbfn, eqv_pdbfn)
for fname in (ref_pdbfn, eqv_pdbfn):
if not os.path.isfile(fname):
logging.warning("Missing file: %s", fname)
raise
except subprocess.CalledProcessError, exc:
raise RuntimeError("TMalign failed (returned %s):\n%s"
% (exc.returncode, exc.output))
tm_seqpair = read_tmalign_as_seqrec_pair(tm_output,
ref_pdbfn, eqv_pdbfn)
allpairs.append(tm_seqpair)
# In case of 2 structs, no need to combine alignments -- we're done
if len(allpairs) == 1:
recs = allpairs[0][:2]
return alnutils.remove_empty_cols(recs)
# 2. Resolve MST pairs & write seed tempfiles
tmp_seed_fnames = []
for seedpair in mst_pairs(allpairs):
# fd, seedfn = tempfile.mkstemp(text=True)
# SeqIO.write(seedpair, seedfn, 'fasta')
# SeqIO.write(seedpair, os.fdopen(fd), 'fasta')
with tempfile.NamedTemporaryFile('w+', delete=False) as handle:
SeqIO.write(seedpair, handle, 'fasta')
tmp_seed_fnames.append(handle.name)
# 3. Use MAFFT to combine TMalign'd pairs into a multiple alignment;
seq_fd, seq_fname = tempfile.mkstemp(text=True)
# Create a blank file to appease MAFFT
os.write(seq_fd, '')
