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Just a simple kseq.h binding

Project description


Just a fasta/q parser based on kseq.h for CPython and PyPy.

Install with:

pip install fastx

Example use:

import fastx
for name, seq, qual for 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.


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

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