API Reference¶

A fast GenBank I/O library based on the gb-io Rust crate.

Example

Load all the GenBank records from a single file, and print their accession:

>>> import gb_io
>>> records = gb_io.load("tests/data/AY048670.1.gb")
>>> print([record.accession for record in records])
['AY048670']

Iterate over records inside a gzip compressed GenBank file, and display the accession and sequence length of each record larger than 400,000bp:

>>> import gb_io
>>> import gzip
>>> with gzip.open("tests/data/JAOQKG01.1.gb.gz", "rb") as reader:
...     for record in gb_io.iter(reader):
...         if len(record.sequence) > 400000:
...             print(record.name, len(record.sequence))
JAOQKG010000001 754685
JAOQKG010000002 569365
JAOQKG010000003 418835
JAOQKG010000004 418347

Functions¶

`gb_io.load`	Load all GenBank records from the given path or file handle.
`gb_io.iter`	Iterate over the GenBank records in the given file or file handle.
`gb_io.dump`	Write one or more GenBank records to the given path or file handle.

Classes¶

Record¶

`gb_io.Record`	A single GenBank record.
`gb_io.Feature`	A feature located somewhere in the record.
`gb_io.Reference`	A reference for a record.
`gb_io.Source`	The source of a GenBank record.
`gb_io.Qualifier`	A single key-value qualifier for a `Feature`.

Locations¶

`gb_io.Location`	A base location for a `Feature`.
`gb_io.Between`	A location for a `Feature` located between two consecutive positions.
`gb_io.Bond`	A location for a `Feature` corresponding to a bond between locations.
`gb_io.Complement`	A location for a `Feature` on the opposite strand of a given `Location`.
`gb_io.External`	A location for a `Feature` located in an external record.
`gb_io.Join`	A location for a `Feature` consisting in joined sequence spans.
`gb_io.OneOf`	A location for a `Feature` located at one of the given locations.
`gb_io.Order`	A location for a `Feature` over disjoint locations in the given order.
`gb_io.Range`	A location for a `Feature` spanning over a range of consecutive positions.

Reader¶

gb_io.RecordReader

An iterator over the Record contained in a file.