def __init__(self, handle, record2title=None):
"""Create a LMAT output writer
Arguments:
- handle - Handle to an output file, e.g. as returned
by open(filename, 'w')
- record2title - Optional function to return the text to be
used for the title line of each record. By default
a combination of the record.id and record.description
is used. If the record.description starts with the
record.id, then just the record.description is used.
You can either use::
handle = open(filename, 'w')
writer = LmatOutWriter(handle)
writer.write_file(myRecords)
handle.close()
Or, follow the sequential file writer system, for example::
handle = open(filename, 'w')
writer = LmatOutWriter(handle)
writer.write_header() # does nothing for LMAT output files
...
Multiple writer.write_record() and/or writer.write_records() calls
...
writer.write_footer() # does nothing for LMAT out files
handle.close()
"""
SequentialSequenceWriter.__init__(self, handle)
self.record2title = record2title
def write_footer(self):
"""Close the root node and finish the XML document."""
SequentialSequenceWriter.write_footer(self)
self.xml_generator.endElement("seqXML")
self.xml_generator.endDocument()
def write_footer(self):
"""Close the root node and finish the XML document."""
SequentialSequenceWriter.write_footer(self)
self.xml_generator.endElement("seqXML")
self.xml_generator.endDocument()
def write_header(self):
"""Write root node with document metadata."""
SequentialSequenceWriter.write_header(self)
attrs = {
"xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"xsi:noNamespaceSchemaLocation":
"http://www.seqxml.org/0.4/seqxml.xsd",
"seqXMLversion": "0.4"
}
if self.source is not None:
attrs["source"] = self.source
if self.source_version is not None:
attrs["sourceVersion"] = self.source_version
if self.species is not None:
if not isinstance(self.species, basestring):
raise TypeError("species should be of type string")
attrs["speciesName"] = self.species
if self.ncbiTaxId is not None:
if not isinstance(self.ncbiTaxId, (basestring, int)):
raise TypeError("ncbiTaxID should be of type string or int")
attrs["ncbiTaxID"] = self.ncbiTaxId
self.xml_generator.startElement("seqXML", AttributesImpl(attrs))
def __init__(self, handle, source=None, source_version=None,
species=None, ncbiTaxId=None):
"""Create Object and start the xml generator."""
SequentialSequenceWriter.__init__(self, handle)
self.xml_generator = XMLGenerator(handle, "utf-8")
self.xml_generator.startDocument()
self.source = source
self.source_version = source_version
self.species = species
self.ncbiTaxId = ncbiTaxId
def __init__(self,
handle,
source=None,
source_version=None,
species=None,
ncbiTaxId=None):
"""Create Object and start the xml generator."""
SequentialSequenceWriter.__init__(self, handle)
self.xml_generator = XMLGenerator(handle, "utf-8")
self.xml_generator.startDocument()
self.source = source
self.source_version = source_version
self.species = species
self.ncbiTaxId = ncbiTaxId
def __init__(self, handle, wrap=60, record2title=None, code=None):
"""Create a PIR writer.
Arguments:
- handle - Handle to an output file, e.g. as returned
by open(filename, "w")
- wrap - Optional line length used to wrap sequence lines.
Defaults to wrapping the sequence at 60 characters
Use zero (or None) for no wrapping, giving a single
long line for the sequence.
- record2title - Optional function to return the text to be
used for the title line of each record. By default
a combination of the record.id, record.name and
record.description is used.
- code - Optional sequence code must be one of P1, F1,
D1, DL, DC, RL, RC, N3 and XX. By default None is used,
which means auto detection based on record alphabet.
You can either use::
handle = open(filename, "w")
writer = PirWriter(handle)
writer.write_file(myRecords)
handle.close()
Or, follow the sequential file writer system, for example::
handle = open(filename, "w")
writer = PirWriter(handle)
writer.write_header() # does nothing for PIR files
...
Multiple writer.write_record() and/or writer.write_records() calls
...
writer.write_footer() # does nothing for PIR files
handle.close()
"""
SequentialSequenceWriter.__init__(self, handle)
self.wrap = None
if wrap:
if wrap < 1:
raise ValueError(
"wrap should be None, 0, or a positive integer")
self.wrap = wrap
self.record2title = record2title
self.code = code
def __init__(self, handle, wrap=60, record2title=None, code=None):
"""Create a PIR writer.
Arguments:
- handle - Handle to an output file, e.g. as returned
by open(filename, "w")
- wrap - Optional line length used to wrap sequence lines.
Defaults to wrapping the sequence at 60 characters
Use zero (or None) for no wrapping, giving a single
long line for the sequence.
- record2title - Optional function to return the text to be
used for the title line of each record. By default
a combination of the record.id, record.name and
record.description is used.
- code - Optional sequence code must be one of P1, F1,
D1, DL, DC, RL, RC, N3 and XX. By default None is used,
which means auto detection based on record alphabet.
You can either use::
handle = open(filename, "w")
writer = PirWriter(handle)
writer.write_file(myRecords)
handle.close()
Or, follow the sequential file writer system, for example::
handle = open(filename, "w")
writer = PirWriter(handle)
writer.write_header() # does nothing for PIR files
...
Multiple writer.write_record() and/or writer.write_records() calls
...
writer.write_footer() # does nothing for PIR files
handle.close()
"""
SequentialSequenceWriter.__init__(self, handle)
self.wrap = None
if wrap:
if wrap < 1:
raise ValueError
self.wrap = wrap
self.record2title = record2title
self.code = code
def __init__(self, handle, wrap=60, record2title=None):
"""Create a Fasta writer.
Arguements:
- handle - Handle to an output file, e.g. as returned
by open(filename, "w")
- wrap - Optional line length used to wrap sequence lines.
Defaults to wrapping the sequence at 60 characters
Use zero (or None) for no wrapping, giving a single
long line for the sequence.
- record2title - Optional function to return the text to be
used for the title line of each record. By default
a combination of the record.id and record.description
is used. If the record.description starts with the
record.id, then just the record.description is used.
You can either use::
handle = open(filename, "w")
writer = FastaWriter(handle)
writer.write_file(myRecords)
handle.close()
Or, follow the sequential file writer system, for example::
handle = open(filename, "w")
writer = FastaWriter(handle)
writer.write_header() # does nothing for Fasta files
...
Multiple writer.write_record() and/or writer.write_records() calls
...
writer.write_footer() # does nothing for Fasta files
handle.close()
"""
SequentialSequenceWriter.__init__(self, handle)
self.wrap = None
if wrap:
if wrap < 1:
raise ValueError
self.wrap = wrap
self.record2title = record2title
def __init__(self, handle, wrap=60, record2title=None):
"""Create a Fasta writer.
Arguments:
- handle - Handle to an output file, e.g. as returned
by open(filename, "w")
- wrap - Optional line length used to wrap sequence lines.
Defaults to wrapping the sequence at 60 characters
Use zero (or None) for no wrapping, giving a single
long line for the sequence.
- record2title - Optional function to return the text to be
used for the title line of each record. By default
a combination of the record.id and record.description
is used. If the record.description starts with the
record.id, then just the record.description is used.
You can either use::
handle = open(filename, "w")
writer = FastaWriter(handle)
writer.write_file(myRecords)
handle.close()
Or, follow the sequential file writer system, for example::
handle = open(filename, "w")
writer = FastaWriter(handle)
writer.write_header() # does nothing for Fasta files
...
Multiple writer.write_record() and/or writer.write_records() calls
...
writer.write_footer() # does nothing for Fasta files
handle.close()
"""
SequentialSequenceWriter.__init__(self, handle)
self.wrap = None
if wrap:
if wrap < 1:
raise ValueError
self.wrap = wrap
self.record2title = record2title
def write_header(self):
"""Write root node with document metadata."""
SequentialSequenceWriter.write_header(self)
attrs = {"xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"xsi:noNamespaceSchemaLocation": "http://www.seqxml.org/0.4/seqxml.xsd",
"seqXMLversion": "0.4"}
if self.source is not None:
attrs["source"] = self.source
if self.source_version is not None:
attrs["sourceVersion"] = self.source_version
if self.species is not None:
if not isinstance(self.species, basestring):
raise TypeError("species should be of type string")
attrs["speciesName"] = self.species
if self.ncbiTaxId is not None:
if not isinstance(self.ncbiTaxId, (basestring, int)):
raise TypeError("ncbiTaxID should be of type string or int")
attrs["ncbiTaxID"] = self.ncbiTaxId
self.xml_generator.startElement("seqXML", AttributesImpl(attrs))
def __init__(self, handle):
SequentialSequenceWriter.__init__(self, handle)
def __init__(self, handle):
"""Initialize the class."""
SequentialSequenceWriter.__init__(self, handle)
def __init__(self, handle):
SequentialSequenceWriter.__init__(self, handle)
def __init__(self, handle):
"""Initialize the class."""
SequentialSequenceWriter.__init__(self, handle)