pyabif 0.3.0

A Python ABIF reader

A Python ABIF (Applied Biosystems Genetic Analysis Data File Format) reader, based on 07/2006 specification.

ABIF is a directory of items, where every item is identified by unique tag and number.

Interface

ABIF is a class with attributes corresponding to name/number items:

>>> from pyabif import ABIF

>>> abif = ABIF('abif.fsa')
>>> abif.User1
joe

>>> abif.DATA1
...

…, or for 1 numbered items this also works:

>>> abif.DATA
...

For items described in 07/2006 specification, there is available description:

>>> help(ABIF.DATA)
Help on property:

    Channel 1 raw data

…, or:

>>> abif.describe('DATA')
'Channel 1 raw data'

Console script

pyABIF can be used as a console script:

$ pyabif abif.fsa
Converted to txt

$ ls abif
abif.fsa
abif.fsa.csv.zip

For usage help:

$ pyabif --help
Usage: pyabif [OPTIONS] [PATTERNS]...

Converts PATTERNS from ABIF to txt format

PATTERNS are glob filenames of ABIF files to convert.

Options:
-f, --force                     Force conversion even if resulting file
                                already exists  [default: False]

-b, --batch                     Combine data files in batches  [default:
                                False]

-d, --digits INTEGER            Number of digits for migration times
                                [default: 3]

-u, --migration-units [seconds|minutes]
                                Migration units  [default: minutes]
--help                          Show this message and exit.