gnk-fastasort 0.1.0

A package to create a preferred order of a FASTA scaffolds, useful for PretextSnapshot and SAMTOOLS reordering.

gnk_fastasort

A package to create a preferred order of a FASTA scaffolds, useful for PretextSnapshot and SAMTOOLS reordering.

This will reorganise a fasta file into groupings, based on chromosome naming. So unlocs of SUPER_1 will be re-ordered alongside it in size order. Other unlocs will be arranged in size order, after everything else.

Installation

git clone https://github.com/sanger-tol/gnk_fastasort.git

cd gnk_fastasort

pip install ./

fastasort -h

Usage

This script can be used in two ways, both however rely on the underlying naming of the fasta being SUPER_* style. In neither case is a fasta file required, it is designed to work in conjunction with SAMTOOLS faidx which will can re-organise a fasta given a tsv file of names. This tool emits a tsv of names, original naming, parent molecule and length or just names.

For example, a fasta fai file where scaffolds are named SUPER_* or a GCA accessioned fasta which was originally named SUPER_* (this is visible from the sequence report on ncbi.).

For genomes stored on NCBI and are accessioned. You can use the --gca_accession to call the API and download a sequence report.

fastasort --gca_accession GCA_964017025.1

For local fasta names where headers are SUPER_1, SUPER_2, SUPER_2_unloc_1 e.g. SUPER_* style, you can run:

fastasort --index {ASSEMBLY}.fa.fai