Tiny FASTA package, without dependencies, for processing biological sequence files.
Python package for working with biological sequences from FASTA files.
- Documentation: http://tinyfasta.readthedocs.org/en/latest/
- GitHub: https://github.com/tjelvar-olsson/tinyfasta
- PyPI: https://pypi.python.org/pypi/tinyfasta
- Free software: MIT License
- Easy to use: intuitive API for parsing, searching and writing FASTA files
- Lightweight: no dependencies outside Python’s standard library
- Cross-platform: Linux, Mac and Windows are all supported
- Works with with Python 2.7, 3.2, 3.3, and 3.4
To install the TinyFasta package:
sudo pip install tinyfasta
To parse a FASTA file:
>>> from tinyfasta import FastaParser >>> for fasta_record in FastaParser("tests/data/dummy.fasta"): ... if fasta_record.description.contains('seq1'): ... print(fasta_record) ... >seq1|contains 2x78 A's AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
To create a FASTA record:
>>> from tinyfasta import FastaRecord >>> sequence = "C" * 100 >>> fasta_record = FastaRecord.create("My Sequence", sequence) >>> print(fasta_record) >My Sequence CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCC