Just a fasta/q parser based on kseq.h for CPython and PyPy.
Install with:
pip install cffi
pip install fastx
Example use:
from fastx import Fastx
for name, seq, qual in Fastx(filename):
print(">{}\n{}".format(name, seq))
This library was inspired by the benchmarking page below and that the existing fastest entry for python works only on CPython. It is not intended for general use.
https://github.com/lh3/biofast
Line profiling the previous code we find program spent as much time adding python objects together as it does in the pyfastx package:
Line # Hits Time Per Hit % Time Line Contents
==============================================================
28 @profile
29 def main():
30 1 21.0 21.0 0.0 n, slen, qlen = 0, 0, 0
31 5682011 7366975.0 1.3 47.9 for name, seq, qual in pyfastx.Fastq(sys.argv[1], build_index=False):
32 5682010 2324629.0 0.4 15.1 n += 1
33 5682010 2783887.0 0.5 18.1 slen += len(seq)
34 5682010 2909447.0 0.5 18.9 qlen += qual and len(qual) or 0
35 1 158.0 158.0 0.0 print('{}\t{}\t{}'.format(n, slen, qlen))
This modules works both under CPython and PyPy, unlike pyfastx which is strictly a CPython extension. When using PyPy, the difference between the Python and C implementation is narrowed dramatically.
Running cpython
5682010 568201000 568201000
real 0m11.444s
user 0m10.944s
sys 0m0.284s
Running pypy
5682010 568201000 568201000
real 0m1.973s
user 0m1.555s
sys 0m0.258s
Running C
5682010 568201000 568201000
real 0m1.764s
user 0m1.508s
sys 0m0.217s