biotite.sequence.io.genbank

This subpackage is used for reading/writing information (especially sequence features) from/to files in the GenBank and GenPept format.

Content

GenBankFile

This class represents a file in GenBank format (including GenPept).

MultiFile

This class represents a file in GenBank or GenPept format, that contains multiple entries, for more than one UID.

get_accession

Parse the ACCESSION field of a GenBank or GenPept file.

get_annotated_sequence

Get an annotated sequence by combining the ANNOTATION and ORIGIN fields of a GenBank file.

get_annotation

Get the sequence annotation from the FEATURES field of a GenBank file.

get_db_link

Parse the DBLINK field of a GenBank or GenPept file.

get_definition

Parse the DEFINITION field of a GenBank or GenPept file.

get_gi

Parse the GI from the VERSION field of a GenBank or GenPept file.

get_locus

Parse the LOCUS field of a GenBank or GenPept file.

get_sequence

Get the sequence from the ORIGIN field of a GenBank file.

get_source

Parse the SOURCE field of a GenBank or GenPept file.

get_version

Parse the version from the VERSION field of a GenBank or GenPept file.

set_annotated_sequence

Set the FEATURES and ORIGIN fields of a GenBank file with the annotation and sequence of an annotated sequence.

set_annotation

Set the FEATURES field of a GenBank file with an annotation.

set_locus

Set the LOCUS field of a GenBank file.

set_sequence

Set the ORIGIN field of a GenBank file with a sequence.