# Bio.GenBank.Record module

Hold GenBank data in a straightforward format.

Classes:

  - Record - All of the information in a GenBank record.

  - Reference - hold reference data for a record.

  - Feature - Hold the information in a Feature Table.

  - Qualifier - Qualifiers on a Feature.

class Bio.GenBank.Record.Record

  Bases: `object`

  Hold GenBank information in a format similar to the original record.

  The Record class is meant to make data easy to get to when you are just interested in looking at GenBank data.

  Attributes:

    - locus - The name specified after the LOCUS keyword in the GenBank record. This may be the accession number, or a clone id or something else.

    - size - The size of the record.

    - residue_type - The type of residues making up the sequence in this record. Normally something like RNA, DNA or PROTEIN, but may be as esoteric as ‘ss-RNA circular’.

    - data_file_division - The division this record is stored under in GenBank (ie. PLN -> plants; PRI -> humans, primates; BCT -> bacteria…)

    - date - The date of submission of the record, in a form like ‘28-JUL-1998’

    - accession - list of all accession numbers for the sequence.

    - nid - Nucleotide identifier number.

    - pid - Proteint identifier number

    - version - The accession number + version (ie. AB01234.2)

    - db_source - Information about the database the record came from

    - gi - The NCBI gi identifier for the record.

    - keywords - A list of keywords related to the record.

    - segment - If the record is one of a series, this is info about which segment this record is (something like ‘1 of 6’).

    - source - The source of material where the sequence came from.

    - organism - The genus and species of the organism (ie. ‘Homo sapiens’)

    - taxonomy - A listing of the taxonomic classification of the organism, starting general and getting more specific.

    - references - A list of Reference objects.

    - comment - Text with any kind of comment about the record.

    - features - A listing of Features making up the feature table.

    - base_counts - A string with the counts of bases for the sequence.

    - origin - A string specifying info about the origin of the sequence.

    - sequence - A string with the sequence itself.

    - contig - A string of location information for a CONTIG in a RefSeq file

    - project - The genome sequencing project numbers (will be replaced by the dblink cross-references in 2009).

    - dblinks - The genome sequencing project number(s) and other links. (will replace the project information in 2009).

  GB_LINE_LENGTH = 79
  GB_BASE_INDENT = 12
  GB_FEATURE_INDENT = 21
  GB_INTERNAL_INDENT = 2
  GB_OTHER_INTERNAL_INDENT = 3
  GB_FEATURE_INTERNAL_INDENT = 5
  GB_SEQUENCE_INDENT = 9
  BASE_FORMAT = '%-12s'
  INTERNAL_FORMAT = ' %-10s'
  OTHER_INTERNAL_FORMAT = ' %-9s'
  BASE_FEATURE_FORMAT = '%-21s'
  INTERNAL_FEATURE_FORMAT = ' %-16s'
  SEQUENCE_FORMAT = '%9s'
  __init__()

    Initialize the class.

  __str__()

    Provide a GenBank formatted output option for a Record.

    The objective of this is to provide an easy way to read in a GenBank record, modify it somehow, and then output it in ‘GenBank format.’ We are striving to make this work so that a parsed Record that is output using this function will look exactly like the original record.

    Much of the output is based on format description info at:

    ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt

  __firstlineno__ = 98
  __static_attributes__ = ('accession', 'base_counts', 'comment', 'contig', 'data_file_division', 'date', 'db_source', 'dblinks', 'definition', 'features', 'gi', 'keywords', 'locus', 'molecule_type', 'nid', 'organism', 'origin', 'pid', 'primary', 'projects', 'references', 'residue_type', 'segment', 'sequence', 'size', 'source', 'taxonomy', 'topology', 'version', 'wgs', 'wgs_scafld')

class Bio.GenBank.Record.Reference

  Bases: `object`

  Hold information from a GenBank reference.

  Attributes:

    - number - The number of the reference in the listing of references.

    - bases - The bases in the sequence the reference refers to.

    - authors - String with all of the authors.

    - consrtm - Consortium the authors belong to.

    - title - The title of the reference.

    - journal - Information about the journal where the reference appeared.

    - medline_id - The medline id for the reference.

    - pubmed_id - The pubmed_id for the reference.

    - remark - Free-form remarks about the reference.

  __init__()

    Initialize the class.

  __str__()

    Convert the reference to a GenBank format string.

  __firstlineno__ = 498
  __static_attributes__ = ('authors', 'bases', 'consrtm', 'journal', 'medline_id', 'number', 'pubmed_id', 'remark', 'title')

class Bio.GenBank.Record.Feature(key='', location='')

  Bases: `object`

  Hold information about a Feature in the Feature Table of GenBank record.

  Attributes:

    - key - The key name of the feature (ie. source)

    - location - The string specifying the location of the feature.

    - qualifiers - A list of Qualifier objects in the feature.

  __init__(key='', location='')

    Initialize the class.

  __repr__()

    Representation of the object for debugging or logging.

  __str__()

    Return feature as a GenBank format string.

  __firstlineno__ = 609
  __static_attributes__ = ('key', 'location', 'qualifiers')

class Bio.GenBank.Record.Qualifier(key='', value='')

  Bases: `object`

  Hold information about a qualifier in a GenBank feature.

  Attributes:

    - key - The key name of the qualifier (ie. /organism=)

    - value - The value of the qualifier (“Dictyostelium discoideum”).

  __init__(key='', value='')

    Initialize the class.

  __repr__()

    Representation of the object for debugging or logging.

  __str__()

    Return feature qualifier as a GenBank format string.

  __firstlineno__ = 640
  __static_attributes__ = ('key', 'value')

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