def GroupFastaParser(data,
label_to_name,
group_key="Group",
aligned=False,
moltype=ASCII,
done_groups=None,
DEBUG=False):
"""yields related sequences as a separate seq collection
Arguments:
- data: line iterable data source
- label_to_name: LabelParser callback
- group_key: name of group key in RichLabel.Info object
- aligned: whether sequences are to be considered aligned
- moltype: default is ASCII
- done_groups: series of group keys to be excluded
"""
done_groups = [[], done_groups][done_groups is not None]
parser = MinimalFastaParser(data,
label_to_name=label_to_name,
finder=XmfaFinder)
group_ids = []
current_collection = {}
for label, seq in parser:
seq = moltype.makeSequence(seq, Name=label, Info=label.Info)
if DEBUG:
print "str(label) ", str(label), "repr(label)", repr(label)
if not group_ids or label.Info[group_key] in group_ids:
current_collection[label] = seq
if not group_ids:
group_ids.append(label.Info[group_key])
else:
# we finish off check of current before creating a collection
if group_ids[-1] not in done_groups:
info = Info(Group=group_ids[-1])
if DEBUG:
print "GroupParser collection keys", current_collection.keys(
)
seqs = cogent.LoadSeqs(data=current_collection,
moltype=moltype,
aligned=aligned)
seqs.Info = info
yield seqs
current_collection = {label: seq}
group_ids.append(label.Info[group_key])
info = Info(Group=group_ids[-1])
seqs = cogent.LoadSeqs(data=current_collection,
moltype=moltype,
aligned=aligned)
seqs.Info = info
yield seqs
def get_alignment_tree(fname):
"""Build a neighbour joining tree"""
from cogent.phylo import distance, nj
from cogent.evolve.models import HKY85, F81
al = cogent.LoadSeqs(fname, format='fasta')
d = distance.EstimateDistances(al, submodel=F81())
d.run(show_progress=False)
mytree = nj.nj(d.getPairwiseDistances())
mytree = mytree.balanced()
print(mytree.asciiArt())
print
'''from cogent.draw import dendrogram
p = dendrogram.SquareDendrogram(mytree)
p.drawToPDF('tree-scaled.pdf', 500, 400, stroke_width=2.0,
shade_param = 'r', max_value = 1.0,)'''
return
def main():
fdir = sys.argv[1]
odir = sys.argv[2]
mkdir_p(odir)
for fname in glob.iglob("{0}/*.fasta".format(fdir)):
groupName = fname.split(os.path.sep)[-1].rstrip(".fasta")
print("group {0}".format(groupName))
try:
seqs = cogent.LoadSeqs(fname,
moltype=cogent.PROTEIN,
aligned=False)
except Exception as e:
print(e)
exit(0)
aln = align_unaligned_seqs(seqs, cogent.PROTEIN)
t = build_tree_from_alignment(aln, cogent.PROTEIN)
print("tree for group {0}".format(str(t)))
with open(os.path.sep.join([odir, groupName + ".nwk"]), 'wb') as ofile:
ofile.write(str(t).replace("'", ""))
def reconstruct(lf, aln, tree, locus=None):
if tree.isTip():
y = tree.Name
P = lf.getPsubForEdge(y, locus=locus)
j = str(aln.NamedSeqs[y])
if 'N' in j:
js = lf.model.getAlphabet().resolveAmbiguity(j)
L = lambda i: max(P[i, j] for j in js)
def C(i):
j = argmax([P[i, j] for j in js])
return js[j]
else:
L = lambda i: P[i, j]
C = lambda i: j
tree.C = C
return L
Ls = [reconstruct(lf, aln, c, locus=locus) for c in tree.Children]
alphabet = list(lf.model.getAlphabet())
calcedLs = {j: prod([L(j) for L in Ls]) for j in alphabet}
if tree.isRoot():
pi = lf.getMotifProbs()
j = argmax([pi[j] * calcedLs[j] for j in alphabet])
tree.anc = alphabet[j]
result = [(tree.Name, tree.anc)]
for child in tree.Children:
_get_anc(child, result)
return cogent.LoadSeqs(data=result)
P = lf.getPsubForEdge(tree.Name, locus=locus)
L = lambda i: max(P[i, j] * calcedLs[j] for j in alphabet)
def C(i):
j = argmax([P[i, j] * calcedLs[j] for j in alphabet])
return alphabet[j]
tree.C = C
return L
def main():
arguments = docopt(__doc__, version='BuildSingleTree v1.0')
print(arguments)
netname = arguments['<network>']
seqname = arguments['<seqfile>']
ofname = arguments['-o']
print("creating tree for {0}".format(netname))
print("using sequences from {0}".format(seqname))
G = nx.read_adjlist(netname)
try:
seqs = cogent.LoadSeqs(seqname, moltype=cogent.PROTEIN, aligned=False)
except Exception as e:
print(e)
sys.exit(0)
aln = align_unaligned_seqs(seqs, cogent.PROTEIN)
t = build_tree_From_alignment(aln, cogent.PROTEIN)
print("tree = {0}".format( str(t) ) )
with open( os.path.sep.join( [ "all" ] ), 'wb') as ofile:
ofile.write( str(t).replace("'","") )