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https://github.com/kdm9/blindschleiche
31 bioinformatics utilities in a trenchcoat
https://github.com/kdm9/blindschleiche
Last synced: 19 days ago
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31 bioinformatics utilities in a trenchcoat
- Host: GitHub
- URL: https://github.com/kdm9/blindschleiche
- Owner: kdm9
- Created: 2022-07-02T07:49:03.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-10-10T15:52:28.000Z (about 1 month ago)
- Last Synced: 2024-10-11T19:22:41.609Z (about 1 month ago)
- Language: Python
- Homepage:
- Size: 164 KB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# blindschleiche
A collection of bioinformatics / sequence utilities needed for my research, and hopefully useful for yours.
[](https://zenodo.org/doi/10.5281/zenodo.10049825)
## Install
```
pip install blindschleiche
# or for the current main branch:
# pip install git+https://github.com/kdm9/blindschleiche.git
```
## Usage
```
USAGE: blsl [options...]
Where 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
pansn-rename: Add, remove, or modify PanSN-style prefixes to contig/chromosome names in references
genigvjs: Generate a simple IGV.js visualisation of some bioinf files.
ildemux: Demultiplex modern illumina reads from read headers.
ilsample: Sample a fraction of read pairs from an interleaved fastq file
regionbed: Make a bed/region file of genome windows
uniref-acc2taxid: Make a ncbi-style acc2taxid.map file for a uniref fasta
nstitch: Combine R1 + R2 into single sequences, with an N in the middle
gg2k: Summarise a table with GreenGenes-style lineages into a kraken-style report.
equalbestblast: Output only the best blast hits.
tabcat: Concatenate table (c/tsv) files, adding the filename as a column
esearchandfetch: Use the Entrez API to search for and download something. A CLI companion to the NCBI search box
deepclust2fa: Split a .faa by the clusters diamond deepclust finds
farename: Rename sequences in a fasta file sequentially
gffcat: Concatenate GFF3 files, resepcting header lines and FASTA sections
gffparse: Format a GFF sanely
gffcsqify: Format a reasonably compliant GFF for use with bcftools csq
gfftagsane: Sanitise a messy gff attribute column to just simple tags
liftoff-gff3: Obtain an actually-useful GFF3 from Liftoff by fixing basic GFF3 format errors
ebiosra2rl2s: INTERNAL: MPI Tübingen tool. Make a runlib-to-sample map table from ebio sra files
galhist: Make a summary histogram of git-annex-list output
pairslash: Add an old-style /1 /2 pair indicator to paired-end fastq files
vcfstats: Use bcftools to calculate various statistics, outputing an R-ready table
vcfparallel: Parallelise a bcf processing pipeline across regions
shannon-entropy: Calculate Shannon's entropy (in bits) at each column of one or more alignments
fastasanitiser: Sanitise fasta IDs to something sane, then back again
tidyqc: What if MultiQC was in the tidyverse? (and much worse)
jsonl2csv: Parse jsonlines into a C/TSV
help: Print this help message
Use blsl subtool --help to get help about a specific tool
```
## Why the name Blindschleiche?
1) [They're awesome animals](https://www.google.com/search?q=blindschleiche&tbm=isch)
2) Their English name is Slow Worm, which is appropriate for this set of low-performance tools in Python.
3) All tools implemented in Python must be named with a snake pun, and they're kinda a snake (not really, they're legless lizards)