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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

Release History

This version
History Node

0.2

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0.1.2

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0.1.1

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0.1

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0.0.5

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0.0.4

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0.0.3.1

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0.0.3

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0.0.2

History Node

0.0.1

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Filename, Size & Hash SHA256 Hash Help File Type Python Version Upload Date
pyseqfile-0.2.tar.gz
(1.4 kB) Copy SHA256 Hash SHA256
Source None Nov 21, 2016

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