The simplest possible fasta and fastq parsers I could come up with. Useful for simple manipulations of sequence files without creating complex dependencies.
The fastalite and fastqlite functions return an iterator of
namedtuples, each with attributes id, (the header line before the
first whitespace) description (the entire header line), and seq
(the sequence as a string). fastqlite output also has an attribute
qual containing the quality scores. For example:
from fastalite import fastalite
with open('inseqs.fasta') as infile, open('outseqs.fasta', 'w') as outfile:
for seq in fastalite(infile):
outfile.write('>{}\n{}\n'.format(seq.id, seq.seq))
The fastqlite parser also performs some limited error checking and
raises ValueError when it encounters a malformed record.
The Opener class may be used in place of argparse.FileType to
support transparent reading and writing of compressed files (inferred
from a .gz or .bz2 suffix), for example:
import argparse
from fastalite import Opener, fastalite
parser = argparse.ArgumentParser()
parser.add_argument('infile', type=Opener())
args = parser.parse_args(arguments)
seqs = fastalite(args.infile)
You can perform a few actions on input files using the command line interface. For a list of available commands:
python -m fastalite -h
Compatible with Python versions 2.7 and 3.4+
Install from PyPi using pip:
pip install fastalite
Or install directly from the git repository:
pip install git+https://github.com/nhoffman/fastalite.git
Run all tests like this:
python setup.py test