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 :).
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
Trace object attributes and methods
- String of base-called nucleotide sequence stored in the file.
- String of phred quality characters of the base-called sequence.
- List of phred quality values of the base-called sequence.
- String of the sequence file 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
- Returns metadata stored in the file, accepts keys from
- 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
- Closes the Trace file object.
- Replaces extra ambigous base characters (K, Y, W, M, R, S) with 'N'. Accepts
- Dictionary for determining which metadata are extracted.
- Dictionary that contains the file metadata. The keys are values of
- 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
$ 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
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:
The quality values itself can be trimmed as well:
Viewing the trace file metadata is easy. Use the values from
as the keys in
>>> 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
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.
pip install abifpy, or
- Add the abifpy directory to your
.bashrcto make it persistent)
abifpy is licensed under the MIT License.
Copyright (c) 2011 by Wibowo Arindrarto <firstname.lastname@example.org>
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.