Description:

bed2seq 0.3.3

bed2seq
From a BED file, return the sequences according to the genome supplied
Installation
Solution 1 (Preferred)
Install with pip
pip install bed2seq

Solution 2
Installation from github:
git clone https://github.com/Bio2M/bed2seq.git

The pyfaidx python package is required, install it with pip, apt or your preferred method.
usage
positional arguments:
bed bed file

options:
-h, --help show this help message and exit
-g genome, --genome genome
genome as fasta file
-a APPEND, --append APPEND
enlarge the sequence ('-a 20' append 20 bp on each side)
-r, --remove only with '--append' option, keep only appended part
-n, --nostrand don't reverse complement when strand is '-'
-o OUTPUT, --output OUTPUT
Output file (default: <input_file>-bed2seq.fa)
-v, --version show program's version number and exit

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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