def action(args):
def newname(leaf, newname):
leaf.name = newname
return leaf
tree = Phylo.parse(args.tree, args.tree_type).next()
leafs = (leaf for leaf in tree.get_terminals())
if args.info:
info = DictReader(args.info, fieldnames = ['seqname','newname'])
info = {i['seqname']:i['newname'] for i in info}
# for newick trees :s will be replaced by |s
if args.tree_type == 'newick':
info = {s.replace(':', '|'):n for s,n in info.items()}
leafs = (l for l in leafs if l.name in info)
leafs = (newname(l, info[l.name]) for l in leafs)
if args.remove_word:
leafs = (newname(l, re.sub(args.remove_word, '', l.name)) for l in leafs)
leafs = (newname(l, l.name.strip()) for l in leafs)
leafs = (newname(l, args.add_prefix + l.name) for l in leafs)
leafs = (newname(l, l.name + args.add_suffix) for l in leafs)
# do this last
if args.tree_type == 'newick':
leafs = (newname(l, l.name.replace(' ', '_')) for l in leafs)
# execute changes and write tree
list(leafs)
Phylo.write(tree, args.out, args.tree_type)
def action(args):
def newname(leaf, newname):
leaf.name = newname
return leaf
tree = Phylo.parse(args.tree, args.tree_type).next()
leafs = (leaf for leaf in tree.get_terminals())
if args.info:
info = DictReader(args.info, fieldnames=['seqname', 'newname'])
info = {i['seqname']: i['newname'] for i in info}
# for newick trees :s will be replaced by |s
if args.tree_type == 'newick':
info = {s.replace(':', '|'): n for s, n in info.items()}
leafs = (l for l in leafs if l.name in info)
leafs = (newname(l, info[l.name]) for l in leafs)
if args.remove_word:
leafs = (newname(l, re.sub(args.remove_word, '', l.name))
for l in leafs)
leafs = (newname(l, l.name.strip()) for l in leafs)
leafs = (newname(l, args.add_prefix + l.name) for l in leafs)
leafs = (newname(l, l.name + args.add_suffix) for l in leafs)
# do this last
if args.tree_type == 'newick':
leafs = (newname(l, l.name.replace(' ', '_')) for l in leafs)
# execute changes and write tree
list(leafs)
Phylo.write(tree, args.out, args.tree_type)
print d.keys()
#['origin', 'dep_time', 'flight', 'hour', 'dep_delay', 'distance', 'dest', 'month', 'air_time', 'carrier', 'year', 'arr_delay', 'tailnum', 'arr_time', 'day', 'minute']
### SELECTED KEYS
selected = ["origin", "dest", "distance", "carrier"]
# EXPECTED OUTPUT
# {'carrier': 'UA', 'dest': 'IAH', 'distance': '1400', 'origin': 'EWR'}
### METHOD 1: DEFINE BY THE DICT COMPREHENSION
{k: d[k] for k in selected}
{k: d.get(k) for k in selected}
{k: v for k, v in d.items() if k in selected}
### METHOD 2: DEFINE BY THE DICT CONSTRUCTOR
dict((k, d[k]) for k in selected)
dict(map(lambda k: (k, d[k]), selected))
dict(filter(lambda i: i[0] in selected, d.items()))
### METHOD 3: DEFINE WITH THE ZIP() FUNCTION
dict(zip(selected, [d[k] for k in selected]))
# ITEMGETTER() FUNCTION WITH THE UNPACK OPERATOR (*)
from operator import itemgetter