def FromFileParser(f, format, dialign_recode=False, **kw):
format = format.lower()
if format in XML_PARSERS:
doctype = format
format = 'xml'
else:
doctype = None
if format == 'xml':
source = dom = xml.dom.minidom.parse(f)
if doctype is None:
doctype = str(dom.doctype.name).lower()
if doctype not in XML_PARSERS:
raise FileFormatError("Unsupported XML doctype %s" % doctype)
parser = XML_PARSERS[doctype]
else:
if format not in PARSERS:
raise FileFormatError("Unsupported file format %s" % format)
parser = PARSERS[format]
source = f
for (name, seq) in parser(source, **kw):
if isinstance(seq, basestring):
if dialign_recode:
seq = seq.translate(_lc_to_wc)
if not seq.isupper():
seq = seq.upper()
yield (name, seq)
def FromFileStructureParser(f, format, dialign_recode=False, **kw):
"""
Returns a structure parser for a specified format for given filename.
Arguments:
- filename: name of the structure file
- format: the structure file format
"""
if not type(f) is file:
raise TypeError('%s is not a file' % f)
format = format.lower()
if format in XML_PARSERS:
doctype = format
format = 'xml'
else:
doctype = None
if format == 'xml':
source = dom = xml.dom.minidom.parse(f)
if doctype is None:
doctype = str(dom.doctype.name).lower()
if doctype not in XML_PARSERS:
raise FileFormatError("Unsupported XML doctype %s" % doctype)
parser = XML_PARSERS[doctype]
else:
if format not in PARSERS:
raise FileFormatError("Unsupported file format %s" % format)
parser = PARSERS[format]
source = f
return parser(source, **kw)
def write_to_file(f, entities, format, **kw):
"""Saves a structure in a specified format into a given file handle.
Arguments:
- entities: structure or entities to be written
- filename: name of the structure file
- format: structure file format
"""
format = format.lower()
if format not in WRITERS:
raise FileFormatError("Unsupported file format %s" % format)
writer = WRITERS[format]
writer(f, entities, **kw)
def save_to_filename(alignment, filename, format, **kw):
"""Arguments:
- alignment: to be written
- filename: name of the sequence alignment file
- format: the multiple sequence file format
"""
if format is None:
raise FileFormatError("format not known")
f = open(filename, 'w')
try:
write_alignment_to_file(f, alignment, format, **kw)
except Exception:
try:
os.unlink(filename)
except Exception:
pass
raise
f.close()
def write_alignment_to_file(f, alignment, format, **kw):
format = format.lower()
if format not in WRITERS:
raise FileFormatError("Unsupported file format %s" % format)
writer = WRITERS[format](f)
writer.writealignment(alignment, **kw)