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 __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 __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): """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