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Overview

Over the years most bioinformatics people amass a collection of small utility scripts which make their lives easier. Too often they are kept either in private repositories or as part of a public collection to which noone else can contribute. Biocode is a curated repository of general-use utility scripts my colleagues and I have found useful and want to share with others.

Look below if you want to learn more, contribute code yourself, or just get the scripts.

-- Joshua Orvis

Scope and directory structure

The scope here is intentionally very open. I want to include anything that developers find generally useful. There are no limitations on language choice. For now, the following directories make up the initial groupings but will be expanded as needed:

  • blast - It if uses, massages, or just reformats BLAST output, it goes here.
  • chado - Scripts that are tied into the chado schema (gmod.org) should be found here.
  • fasta - Filtering, converting, size distribution plots, etc.
  • fastq - Utilities for fasta's newer sister format.
  • genbank - Anything related to the GenBank? Flat File Format.
  • general - Utility scripts that may not fit in any other existing directory or don't warrant creation of their own. We should be selective about what we put here and create or use other directories whenever appropriate.
  • gff - Extractions, conversions and manipulations of files in the Generic Feature Format (sequenceontology.org/gff3.shtml)
  • gtf - From Ensembl/WashU, the GTF format is the focus of scripts here.
  • hmm - Merging, manipulating or reading HMM libraries.
  • sandbox - Each committer gets their own personal directory here to add anything they want while testing or waiting to be moved to the production directories.
  • sysadmin - While not specifically bioinformatics, our work tends to be on Unix machines, and utility scripts are often needed to support our work. From file system manipulation to database backup scripts, put your generic sysadmin utilities here.
  • taxonomy - Anything related to taxonomic analysis.

Getting the code

The best way to get the code for now is to just clone it:

git clone https://github.com/jorvis/biocode.git

Problems?

If you encounter any issues please submit to the Issue tracking system and those responsible will be sacked.

Contributing

If you'd like to contribute code to this collection have a look at the Requirements And Convention Guide and then submit a pull request once your code is ready. We'll check your script and pull it into the production directories. If you're not that confident yet we'll happily pull in your sandbox directory if you'd like to add your code to the project but aren't sure if it's ready to be in the production directories yet.