Misc sequence tools in python. These tools are small things which I have at some point needed to write because I couldn't find a solution I liked. This is in no way a comprehensive toolkit. It is a companion to seqhax, execpt that seqhax is written in C/C++ and generally contains tools to handle very large datasets where performance is somewhat important. This is all in python for ease of development, and so typically these tools perform less data- or compute-intensive tasks.
pip install blindschleiche
# or for the current main branch:
# pip install git+https://github.com/kdm9/blindschleiche.git
USAGE: blsl <subtool> [options...]
Where <subtool> is one of:
telogrep: Search contigs for known telomere repeats
n50: Calculate N50 and total length of a set of contigs
falen: Tabulate the lengths of sequences in a FASTA file
mask2bed: The inverse of bedtools maskfasta: softmasked fasta -> unmasked fasta + mask.bed
genigvjs: Generate a simple IGV.js visualisation of some bioinf files.
liftoff-gff3: Obtain an actually-useful GFF3 from Liftoff by fixing basic GFF3 format errors
pansn-rename: Add, remove, or modify PanSN-style prefixes to contig/chromosome names in references
Use blsl subtool --help to get help about a specific tool
- They're awesome animals
- Their English name is Slow Worm, which is appopriate for this set of low-performance tools in Python. Also they're kinda a snake (not really).