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Pyseqfile is a python wrapper on top of [seq_file](https://github.com/noporpoise/seq_file) which allow for reading multiple sequence file formats.

Project description

# pyseqfile

Pyseqfile is a python wrapper on top of [seq_file](https://github.com/noporpoise/seq_file) which allow for reading multiple sequence file formats.

Currently supports:

FASTA & FASTQ

TO DO:

* SAM & BAM (make seq_file with htslib)
* gzipped FASTA
* gzipped FASTQ

# Install

pip install pyseqfile

# Usage

from pyseqfile import Reader

reader = Reader('path/to/seqfile{.fq,.fq,.fa,bam,.sam}')
for r in reader:
print(r)

# Benchmarks

pyseqfile is *much* faster than Biopython.

$ python benchmark.py

Reading 10k lines 100 times: Biopython : 6.6768401420122245s
Reading 10k lines 100 times: seqfile : 0.1060560290061403s

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pyseqfile-0.2.tar.gz (1.4 kB view hashes)

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