TinyFasta

Python package for working with biological sequences from FASTA files.

• Documentation: http://tinyfasta.readthedocs.io
• GitHub: https://github.com/tjelvar-olsson/tinyfasta
• PyPI: https://pypi.python.org/pypi/tinyfasta
• Free software: MIT License

Features

• 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, 3.3, 3.4 and 3.5

Quick Guide

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