fasta.py

The fasta.py python module contains code for reading fasta records from a file.

I know that there is also a fasta parser in BioPython, but I find my own implementation cleaner and easier to use, especially since I use python's iteration mechanism rather than a homegrown iterator as does BioPython. This means that I can use simple for loops for scanning through a fasta file, and not have to use the silly while 1: ... test for None construction.

Usage

To iterate through all records in a file, use:

from fasta import fasta_itr
for rec in fasta_itr(file):
  # do stuff with record
  h = rec.header
  s = rec.sequence
  ...

In this example, file can be either a file object or the name of a file.

To iterate through a slice of the records in a file, use:

from fasta import fasta_slice
for (header,sequence) in fasta_slice(file, start, stop):
  # do stuff with record
  h = rec.header
  s = rec.sequence
  ...

As a final feature, it is possible to index the sequences in an iterator through names:

itr = fasta.fasta_itr(file)
rec1 = itr["foobar"]
slice = fasta.fasta_slice(file,2,4)
rec2 = slice["baz"] 
rec3 = fasta.get_sequence(file,"qux") 

Installation

Download the file and put it somewhere in your PYTHON_PATH.

Contact

Thomas Mailund, <mailund@birc.au.dk>, Bioinformatics Research Center, University of Aarhus.