README.rst

⚠️ unmaintained

A modified version of this module has been merged into the Biopython project, available from version 1.58 onwards. If you already have Biopython version >=1.58, there is no need to use abifpy. Despite that, I am keeping the module available as a stand-alone for personal reasons :).

ABIFPY

Python module for reading ABI Sanger sequencing trace files

abifpy is a python module that extracts sequence and various other data from Applied Biosystem's, Inc. format (ABI) file. The module is python3-compatible and was written based on the official spec released by Applied Biosystems.

abifpy provides the following items:

class Trace(in_file)

Class representing the trace file in_file.

Trace object attributes and methods

seq

String of base-called nucleotide sequence stored in the file.

qual

String of phred quality characters of the base-called sequence.

qual_val

List of phred quality values of the base-called sequence.

id

String of the sequence file name.

name

String of the sample name entered prior to sequencing.

trim(sequence[, cutoff=0.05])

Returns a trimmed sequence using Richard Mott's algorithm (used in phred) with the probability cutoff of 0.05. Can be used on seq, qual, and qual_val.

get_data(key)

Returns metadata stored in the file, accepts keys from tags (see below).

export([out_file="", fmt='fasta'])

Writes a fasta (fmt='fasta'), qual (fmt='qual'), or fastq (fmt='fastq') file from the trace file. Default format is fasta.

close()

Closes the Trace file object.

seq_remove_ambig(seq)

Replaces extra ambigous base characters (K, Y, W, M, R, S) with 'N'. Accepts seq for input.

EXTRACT

Dictionary for determining which metadata are extracted.

data

Dictionary that contains the file metadata. The keys are values of EXTRACT.

tags

Dictionary of tags with values of data directory class instance. Keys are tag name and tag number, concatenated. Use get_data() to access values in each tags entry.

Usage

$ python
>>> from abifpy import Trace
>>> yummy = Trace('tests/3730.ab1')

Or if you want to perform base trimming directly:

>>> yummy = Trace('tests/3730.ab1', trimming=True)

Sequence can be accessed with the seq attribute. Other attributes of note are qual for phred quality characters, qual_val for phred quality values, id for sequencing trace file name, and name for the sample name:

>>> yummy.seq
'GGGCGAGCKYYAYATTTTGGCAAGAATTGAGCTCT...
>>> yummy.qual
'5$%%%\'%%!!!\'!+5;726@>A=3824DESHSS...
>>> yummy.qual_val
[20, 3, 4, 4, 4, 6, 4, 4, 0, 0, 0, 6, 0, 10, 20, 26, 22, 17, 21...
>>> yummy.id
'3730'
>>> yummy.name
'226032_C-ME-18_pCAGseqF'

If trimming was not performed when instantiating, you can still do it afterwards:

>>> yummy.trim(yummy.seq)

The quality values itself can be trimmed as well:

>>> yummy.trim(yummy.qual)

Viewing the trace file metadata is easy. Use the values from EXTRACT as the keys in data:

>>> yummy.data['well']
'B9'
>>> yummy.data['model']
'3730'
>>> yummy.data['run start date']
datetime.date(2009, 12, 12)

metadata not contained in data can be viewed using get_data() with one of the keys in tags as the argument, e.g.:

>>> yummy.get_data('PTYP1')
'96-well'

For more info on the meaning of these tags and the file metadata, consult the official spec.

Installation

• pip install abifpy, or
• Add the abifpy directory to your $PYTHONPATH (in .bashrc to make it persistent)

License

abifpy is licensed under the MIT License.

Copyright (c) 2011 by Wibowo Arindrarto <[email protected]>

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.