germant13 / bit Goto Github PK

These are a collection of one-liners and short scripts I use frequently enough that it's been worth it for me to have them instantly available anywhere. This includes things like:

1. quickly summarizing nucleotide assemblies (bit-summarize-assembly)
2. downloading NCBI assemblies in different formats by just providing accession numbers (bit-dl-ncbi-assemblies)
3. calculating variation in each column of a multiple sequence alignment (bit-calc-variation-in-msa)
4. summarizing GO annotations (bit-summarize-go-annotations)
5. pulling out sequences by their coordinates (bit-extract-seqs-by-coords)
6. splitting a fasta file based on headers (bit-parse-fasta-by-headers)
7. renaming sequences in a fasta (bit-rename-fasta-headers)
8. pulling amino acid or nucleotide sequences out of a GenBank file (bit-genbank-to-AA-seqs / bit-genbank-to-fasta)

And other just convenient things that are nice to have handy like removing those annoying soft line wraps that some fasta files have (bit-remove-wraps) and printing out the column names of a TSV with numbers (bit-colnames) to quickly see which columns need to be provided to things like cut or awk 🙂

In current conda environment:

conda install -c conda-forge -c bioconda -c defaults -c astrobiomike bit

Or if wanted or needed in a separate environment, that can be done with:

conda create -n bit -c conda-forge -c bioconda -c defaults -c astrobiomike bit
conda activate bit

Each command has a help menu accessible by either entering the command alone or by providing -h as the only argument. Once installed, you can see all available commands by entering bit- and pressing tab twice.

If you happen to find this useful in your work and are inclined to cite this toolset, thank you 🙂, and please do so with the following:

Lee, MD. Bioinformatics Tools (bit) 2018. doi.org/10.5281/zenodo.3383647

You can get the version you are using with bit-version.