bed2seq 0.3.0

From a BED file, return the sequences according to the genome supplied

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