A collection of bioinformatics / sequence utilities needed for my research, and hopefully useful for yours.
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:
deepclust2fa: Split a .faa by the clusters diamond deepclust finds
ebiosra2rl2s: INTERNAL: MPI Tübingen tool. Make a runlib-to-sample map table from ebio sra files
equalbestblast: Output only the best blast hits.
esearchandfetch: Use the Entrez API to search for and download something. A CLI companion to the NCBI search box
falen: Tabulate the lengths of sequences in a FASTA file
farename: Rename sequences in a fasta file sequentially
fastasanitiser: Sanitise fasta IDs to something sane, then back again
fqstat: Estimate stats from a fastq file based on the first kilobytes of the file, keeping high accuracy
galhist: Make a summary histogram of git-annex-list output
genebed: Extract a BED file of genes from a GFF
genigvjs: Generate a simple IGV.js visualisation of some bioinf files.
gffattr2tsv: Extract the attributes column into a TSV
gffcat: Concatenate GFF3 files, resepcting header lines and FASTA sections
gffcsqify: Format a reasonably compliant GFF for use with bcftools csq
gffparse: Format a GFF sanely
gfftagsane: Sanitise a messy gff attribute column to just simple tags
gg2k: Summarise a table with GreenGenes-style lineages into a kraken-style report.
ildemux: Demultiplex modern illumina reads from read headers.
ilsample: Sample a fraction of read pairs from an interleaved fastq file
jsonl2csv: Parse jsonlines into a C/TSV
liftoff-gff3: Obtain an actually-useful GFF3 from Liftoff by fixing basic GFF3 format errors
mask2bed: The inverse of bedtools maskfasta: softmasked fasta -> unmasked fasta + mask.bed
n50: Calculate N50 and total length of a set of contigs
nstitch: Combine R1 + R2 into single sequences, with an N in the middle
pairs: Handle paired-end reads, with various transformations.
pairslash: Add an old-style /1 /2 pair indicator to paired-end fastq files (DEPRECATED, use blsl pairs)
pansn-rename: Add, remove, or modify PanSN-style prefixes to contig/chromosome names in references
regionbed: Make a bed/region file of genome windows
shannon-entropy: Calculate Shannon's entropy (in bits) at each column of one or more alignments
tabcat: Concatenate table (c/tsv) files, adding the filename as a column
telogrep: Search contigs for known telomere repeats
tidyqc: What if MultiQC was in the tidyverse? (and much worse)
uniref-acc2taxid: Make a ncbi-style acc2taxid.map file for a uniref fasta
vcfparallel: Parallelise a bcf processing pipeline across regions
vcfreport: vcfreport: Prepare a basic html report about a VCF file
vcfstats: Use bcftools to calculate various statistics, outputing an R-ready table
help: Print this help message
Use blsl subtool --help to get help about a specific tool
- They're awesome animals
- Their English name is Slow Worm, which is appropriate for this set of low-performance tools in Python.
- All tools implemented in Python must be named with a snake pun, and they're kinda a snake (not really, they're legless lizards)