class NewickReader: """ Just a wrapper around Bio.Nexus.Trees to read newick files. In addition, since many of my newick taxon labels are just ncRNA <db_id>s, support database lookup for these IDs as well. """ def __init__(self, filename): self.filename = filename self.tree = None f = open(self.filename, 'r') chunk = f.read() f.close() self.tree = Tree(chunk) def distance(self, taxon1, taxon2): """ Note that here "taxon" simply means whatever the terminal nodes' data are. Since most of my newick files are labeled with <db_id>, it could just be ex: '34969'. """ id1 = self.tree.search_taxon(taxon1) id2 = self.tree.search_taxon(taxon2) return self.tree.distance(id1, id2)
alltaxa = mytreeobj.get_taxa()
badtaxa = []
slowest_inparalogs = {}
for taxon in alltaxa:
if taxon not in oldid_newid.values():
badtaxa.append(taxon)
else:
sp = taxon.split('_bpgseq')[0]
if sp in slowest_inparalogs:
(old_taxon, old_brlen) = slowest_inparalogs[sp]
new_brlen = mytreeobj.node(
mytreeobj.search_taxon(taxon)).get_data().branchlength
if new_brlen < old_brlen:
slowest_inparalogs[sp] = (
taxon, mytreeobj.node(mytreeobj.search_taxon(
taxon)).get_data().branchlength)
badtaxa.append(old_taxon)
else:
badtaxa.append(taxon)
else:
slowest_inparalogs[sp] = (taxon,
mytreeobj.node(
mytreeobj.search_taxon(taxon)
).get_data().branchlength)
alltaxa = mytreeobj.get_taxa()
badtaxa = []
slowest_inparalogs = {}
for taxon in alltaxa:
if taxon not in oldid_newid.values():
badtaxa.append(taxon)
else:
sp = taxon.split('_seqh')[0]
if sp in slowest_inparalogs:
(old_taxon, old_brlen) = slowest_inparalogs[sp]
new_brlen = mytreeobj.node(
mytreeobj.search_taxon(taxon)).get_data().branchlength
if new_brlen < old_brlen:
slowest_inparalogs[sp] = (taxon,
mytreeobj.node(
mytreeobj.search_taxon(taxon)
).get_data().branchlength)
badtaxa.append(old_taxon)
else:
badtaxa.append(taxon)
else:
slowest_inparalogs[sp] = (
taxon, mytreeobj.node(
mytreeobj.search_taxon(taxon)).get_data().branchlength)
