def write(trees, file, format, **kwargs):
"""Write a sequence of trees to file in the given format."""
if isinstance(trees, BaseTree.Tree) or isinstance(trees, BaseTree.Clade):
# Passed a single tree instead of an iterable -- that's OK
trees = [trees]
with File.as_handle(file, 'w+') as fp:
n = getattr(supported_formats[format], 'write')(trees, fp, **kwargs)
return n
def parse(file, format, **kwargs):
"""Iteratively parse a file and return each of the trees it contains.
If a file only contains one tree, this still returns an iterable object that
contains one element.
Example
-------
>>> trees = parse('../../Tests/PhyloXML/apaf.xml', 'phyloxml')
>>> for tree in trees:
... print(tree.rooted)
True
"""
with File.as_handle(file, 'r') as fp:
for tree in getattr(supported_formats[format], 'parse')(fp, **kwargs):
yield tree
def parse_pdb_header(infile):
"""
Returns the header lines of a pdb file as a dictionary.
Dictionary keys are: head, deposition_date, release_date, structure_method,
resolution, structure_reference, journal_reference, author and
compound.
"""
header = []
with File.as_handle(infile, 'r') as f:
for l in f:
record_type = l[0:6]
if (record_type == 'ATOM ' or record_type == 'HETATM'
or record_type == 'MODEL '):
break
else:
header.append(l)
return _parse_pdb_header_list(header)
def parse_pdb_header(infile):
"""
Returns the header lines of a pdb file as a dictionary.
Dictionary keys are: head, deposition_date, release_date, structure_method,
resolution, structure_reference, journal_reference, author and
compound.
"""
header = []
with File.as_handle(infile, 'r') as f:
for l in f:
record_type=l[0:6]
if (record_type=='ATOM ' or record_type=='HETATM' or
record_type=='MODEL '):
break
else:
header.append(l)
return _parse_pdb_header_list(header)
