def impute_ancestors_dnapars(seqs,
gl_seq,
scratch_dir,
gl_name='germline',
verbose=True):
"""
Compute ancestral states via maximum parsimony
@param seqs: list of sequences
@param gl_seq: germline sequence
@param scratch_dir: where to write intermediate dnapars files
@param gl_name: name of germline (must be less than 10 characters long)
@return genes_line: information needed to output imputed germline data
@return seqs_line: information needed to output imputed sequence data
"""
from gctree.bin.phylip_parse import parse_outfile
assert (len(gl_name) < 10)
infile, config, outfile = [
os.path.join(scratch_dir, fname) for fname in [
'infile',
'dnapars.cfg',
'outfile',
]
]
aln = MultipleSeqAlignment([SeqRecord(Seq(gl_seq), id=gl_name)])
# sequence ID must be less than ten characters, but also dnapars sets internal node
# names to 1, 2, 3, ..., so name them numbers descending from 100 million, hoping
# we won't ever have a clone that big...
for idx, seq in enumerate(seqs):
aln.append(SeqRecord(Seq(seq), id=str(99999999 - idx)))
# dnapars uses the name "infile" as default input phylip file
with open(infile, 'w') as phylip_file:
phylip_file.write(aln.format('phylip'))
# and we need to tell it the line where the root sequence occurs
with open(infile, 'r') as phylip_file:
for lineno, line in enumerate(phylip_file):
if line.startswith(gl_name):
naive_idx = str(lineno)
# arcane user options for dnapars
# 'O', naive_idx: the location of the outgroup root
# 'S', 'Y': less thorough search; runs much faster but output is less exhaustive
# 'J', 13, 10: randomize input ("jumble") using seed 13 and jumbling 10 times
# 4: print out steps in each site (to get all nucleotide info)
# 5: print sequences in at all nodes (to get ancestors)
# '.': use dot-differencing for display
# 'Y': accept these options
with open(config, 'w') as cfg_file:
cfg_file.write('\n'.join(
['O', naive_idx, 'S', 'Y', 'J', '13', '10', '4', '5', '.', 'Y']))
# defer to command line to construct parsimony trees and ancestral states
# dnapars has weird behavior if outfile and outtree already exist o_O
cmd = [
'cd', scratch_dir, '&& rm -f outfile outtree && dnapars <',
os.path.basename(config), '> dnapars.log'
]
if verbose:
print "Calling:", " ".join(cmd)
res = subprocess.call([" ".join(cmd)], shell=True)
# phew, finally got some trees
trees = parse_outfile(outfile, countfile=None, naive=gl_name)
# take first parsimony tree
genes_line = []
seq_line = []
for idx, descendant in enumerate(trees[0].traverse('preorder')):
if descendant.is_root():
descendant.name = gl_name
else:
# use dummy name for internal node sequences
descendant.name = '-'.join([descendant.up.name, descendant.name])
if [descendant.up.name,
descendant.up.sequence.lower()] not in genes_line:
genes_line.append(
[descendant.up.name,
descendant.up.sequence.lower()])
seq_line.append([
descendant.up.name, descendant.name,
descendant.sequence.lower()
])
return genes_line, seq_line
