khughitt/cats


cat for sequence files.

License: BSD-2-Clause

Language: Python


cats

pretty print and other basic manipulations for sequence data.

Screenshot

cats screenshot

Installation

pre-requisites

installation:

sudo python setup.py install

Usage

Basic usage:

cats <input file>

Some more examples:

cats --translate -translations-offset -1 sample.fasta
cats -t -n sample.fasta
cats -w 80 sample.fasta
cats --stop-codons 80 sample.fasta

You can also pipe the output into less to page through output:

cats sample.fasta | less

Or grep for an interesting feature and pipe the output into cats:

grep --color='always' "AAUAA" input.fastq | cats

Gzipped files are also supported:

zgrep --color='always' "AAAAA$" input.fastq.gz | cats

Project Statistics

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Repository Size 611 KB
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Open issues 15
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Keith Hughitt

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