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Tiny FASTA package, without dependencies, for processing biological sequence files.

Project Description

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Python package for working with biological sequences from FASTA files.

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, 3.2, 3.3, and 3.4

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

Release history Release notifications

This version
History Node

0.1.0

History Node

0.0.2

History Node

0.0.1

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Filename, size & hash SHA256 hash help File type Python version Upload date
tinyfasta-0.1.0.tar.gz (4.7 kB) Copy SHA256 hash SHA256 Source None Jun 5, 2015

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