# Bio.SeqIO.InsdcIO module

Bio.SeqIO support for the “genbank” and “embl” file formats.

You are expected to use this module via the Bio.SeqIO functions. Note that internally this module calls Bio.GenBank to do the actual parsing of GenBank, EMBL and IMGT files.

See Also: International Nucleotide Sequence Database Collaboration http://www.insdc.org/

GenBank http://www.ncbi.nlm.nih.gov/Genbank/

EMBL Nucleotide Sequence Database http://www.ebi.ac.uk/embl/

DDBJ (DNA Data Bank of Japan) http://www.ddbj.nig.ac.jp/

IMGT (use a variant of EMBL format with longer feature indents) http://imgt.cines.fr/download/LIGM-DB/userman_doc.html http://imgt.cines.fr/download/LIGM-DB/ftable_doc.html http://www.ebi.ac.uk/imgt/hla/docs/manual.html

class Bio.SeqIO.InsdcIO.GenBankIterator(source)

  Bases: `SequenceIterator`

  Parser for GenBank files.

  modes = 't'
  __init__(source)

    Break up a Genbank file into SeqRecord objects.

    Argument source is a file-like object opened in text mode or a path to a file. Every section from the LOCUS line to the terminating // becomes a single SeqRecord with associated annotation and features.

    Note that for genomes or chromosomes, there is typically only one record.

    This gets called internally by Bio.SeqIO for the GenBank file format:

        >>> from Bio import SeqIO
        >>> for record in SeqIO.parse("GenBank/cor6_6.gb", "gb"):
        ...     print(record.id)
        ...
        X55053.1
        X62281.1
        M81224.1
        AJ237582.1
        L31939.1
        AF297471.1

    Equivalently,

        >>> with open("GenBank/cor6_6.gb") as handle:
        ...     for record in GenBankIterator(handle):
        ...         print(record.id)
        ...
        X55053.1
        X62281.1
        M81224.1
        AJ237582.1
        L31939.1
        AF297471.1

  __next__()

    Return the next SeqRecord.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 62
  __parameters__ = ()
  __static_attributes__ = ('records',)

class Bio.SeqIO.InsdcIO.EmblIterator(source)

  Bases: `SequenceIterator`

  Parser for EMBL files.

  modes = 't'
  __init__(source)

    Break up an EMBL file into SeqRecord objects.

    Argument source is a file-like object opened in text mode or a path to a file. Every section from the LOCUS line to the terminating // becomes a single SeqRecord with associated annotation and features.

    Note that for genomes or chromosomes, there is typically only one record.

    This gets called internally by Bio.SeqIO for the EMBL file format:

        >>> from Bio import SeqIO
        >>> for record in SeqIO.parse("EMBL/epo_prt_selection.embl", "embl"):
        ...     print(record.id)
        ...
        A00022.1
        A00028.1
        A00031.1
        A00034.1
        A00060.1
        A00071.1
        A00072.1
        A00078.1
        CQ797900.1

    Equivalently,

        >>> with open("EMBL/epo_prt_selection.embl") as handle:
        ...     for record in EmblIterator(handle):
        ...         print(record.id)
        ...
        A00022.1
        A00028.1
        A00031.1
        A00034.1
        A00060.1
        A00071.1
        A00072.1
        A00078.1
        CQ797900.1

  __next__()

    Return the next SeqRecord.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 112
  __parameters__ = ()
  __static_attributes__ = ('records',)

class Bio.SeqIO.InsdcIO.ImgtIterator(source)

  Bases: `SequenceIterator`

  Parser for IMGT files.

  modes = 't'
  __init__(source)

    Break up an IMGT file into SeqRecord objects.

    Argument source is a file-like object opened in text mode or a path to a file. Every section from the LOCUS line to the terminating // becomes a single SeqRecord with associated annotation and features.

    Note that for genomes or chromosomes, there is typically only one record.

  __next__()

    Return the next SeqRecord.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 168
  __parameters__ = ()
  __static_attributes__ = ('records',)

class Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator(source)

  Bases: `SequenceIterator`

  Parser for GenBank files, creating a SeqRecord for each CDS feature.

  modes = 't'
  __init__(source)

    Break up a Genbank file into SeqRecord objects for each CDS feature.

    Argument source is a file-like object opened in text mode or a path to a file.

    Every section from the LOCUS line to the terminating // can contain many CDS features. These are returned as with the stated amino acid translation sequence (if given).

  __next__()

    Return the next SeqRecord.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 191
  __parameters__ = ()
  __static_attributes__ = ('records',)

class Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator(source)

  Bases: `SequenceIterator`

  Parser for EMBL files, creating a SeqRecord for each CDS feature.

  modes = 't'
  __init__(source)

    Break up a EMBL file into SeqRecord objects for each CDS feature.

    Argument source is a file-like object opened in text mode or a path to a file.

    Every section from the LOCUS line to the terminating // can contain many CDS features. These are returned as with the stated amino acid translation sequence (if given).

  __next__()

    Return the next SeqRecord.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 213
  __parameters__ = ()
  __static_attributes__ = ('records',)

class Bio.SeqIO.InsdcIO.GenBankWriter(target: IO | PathLike | str | bytes)

  Bases: `_InsdcWriter`

  GenBank writer.

  HEADER_WIDTH = 12
  QUALIFIER_INDENT = 21
  STRUCTURED_COMMENT_START = '-START##'
  STRUCTURED_COMMENT_END = '-END##'
  STRUCTURED_COMMENT_DELIM = ' :: '
  LETTERS_PER_LINE = 60
  SEQUENCE_INDENT = 9
  write_record(record)

    Write a single record to the output file.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 576
  __parameters__ = ()
  __static_attributes__ = ()

class Bio.SeqIO.InsdcIO.EmblWriter(target: IO | PathLike | str | bytes)

  Bases: `_InsdcWriter`

  EMBL writer.

  HEADER_WIDTH = 5
  QUALIFIER_INDENT = 21
  QUALIFIER_INDENT_STR = 'FT '
  QUALIFIER_INDENT_TMP = 'FT %s '
  FEATURE_HEADER = 'FH Key Location/Qualifiers\nFH\n'
  LETTERS_PER_BLOCK = 10
  BLOCKS_PER_LINE = 6
  LETTERS_PER_LINE = 60
  POSITION_PADDING = 10
  write_record(record)

    Write a single record to the output file.

  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 1166
  __parameters__ = ()
  __static_attributes__ = ()

class Bio.SeqIO.InsdcIO.ImgtWriter(target: IO | PathLike | str | bytes)

  Bases: `EmblWriter`

  IMGT writer (EMBL format variant).

  HEADER_WIDTH = 5
  QUALIFIER_INDENT = 25
  QUALIFIER_INDENT_STR = 'FT '
  QUALIFIER_INDENT_TMP = 'FT %s '
  FEATURE_HEADER = 'FH Key Location/Qualifiers\nFH\n'
  __abstractmethods__ = frozenset({})
  __annotations__ = {}
  __firstlineno__ = 1521
  __parameters__ = ()
  __static_attributes__ = ()

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