def __init__(self, handle):
"""Creates the writer object
Use the method write_file() to actually record your sequence records."""
SequentialSequenceWriter.__init__(self, handle)
self._ids_written = []
self._length_of_sequences = None
def __init__(self, handle, wrap=60, record2title=None):
"""Create a QUAL 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.
The record2title argument is present for consistency with the
Bio.SeqIO.FastaIO writer class.
"""
SequentialSequenceWriter.__init__(self, handle)
#self.handle = handle
self.wrap = None
if wrap :
if wrap < 1 :
raise ValueError
self.wrap = wrap
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_ersion
if self.species is not None:
if not isinstance(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, wrap=60, record2title=None):
"""Create a QUAL 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.
The record2title argument is present for consistency with the
Bio.SeqIO.FastaIO writer class.
"""
SequentialSequenceWriter.__init__(self, handle)
#self.handle = handle
self.wrap = None
if wrap:
if wrap < 1:
raise ValueError
self.wrap = wrap
self.record2title = record2title
def write_footer(self):
assert self._header_written, "You must call write_header() first"
assert self._record_written, "You have not called write_record() or write_records() yet"
assert not self._footer_written, "You have aleady called write_footer()"
#self._footer_written = True
SequentialSequenceWriter.write_footer(self)
self.handle.write("//\n")
self._footer_written = True
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 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_ersion
if self.species is not None:
if not isinstance(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, wrap=60, record2title=None):
"""Create a Fasta writer.
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 the
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:
myWriter = FastaWriter(open(filename,"w"))
writer.write_file(myRecords)
Or, follow the sequential file writer system, for example:
myWriter = FastaWriter(open(filename,"w"))
writer.write_header() # does nothing for Fasta files
...
Multiple calls to writer.write_record() and/or writer.write_records()
...
writer.write_footer() # does nothing for Fasta files
writer.close()
"""
SequentialSequenceWriter.__init__(self, handle)
#self.handle = 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.
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 the
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:
myWriter = FastaWriter(open(filename,"w"))
writer.write_file(myRecords)
Or, follow the sequential file writer system, for example:
myWriter = FastaWriter(open(filename,"w"))
writer.write_header() # does nothing for Fasta files
...
Multiple calls to writer.write_record() and/or writer.write_records()
...
writer.write_footer() # does nothing for Fasta files
writer.close()
"""
SequentialSequenceWriter.__init__(self, handle)
#self.handle = handle
self.wrap = None
if wrap :
if wrap < 1 :
raise ValueError
self.wrap = wrap
self.record2title = record2title
def write_header(self, count):
"""Must supply the number of records (count)"""
SequentialSequenceWriter.write_header(self) # sets flags
self.handle.write("# STOCKHOLM 1.0\n")
self.handle.write("#=GF SQ %i\n" % count)
