~pfm/gas

Gas Assembles Sequences
Move away from Microsoft Github
da1e5dff — Piotr Filip Mieszkowski 8 years ago
Various minor improvements
3c7766e3 — Piotr F. Mieszkowski 10 years ago
Started using MAKE-MATCH to create match data.

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#GAS

#Basic Information

GAS, which is a recursive acronym and stands for `GAS Assembles Sequences', is a project started during Lisp in Summer Projects 2013.

It's main goal is to collect, edit and match results of DNA sequencing, allowing the user to export the results of matching to a commonly used file format.

For license information, see the LICENSE file.

Don't hesitate to send bug reports using SourceHut issue system --- I will gladly improve GAS and, hopefully, make it a useful utility in some unspecified future.

#Install and Build

To install GAS, you need to do the following:

  1. Install Steel Bank Common Lisp. If you're using GNU/Linux, you can probably find a package for your distribution. For MS Windows users, there is an installer on SBCL's Download page.
  2. Fetch GAS source code using Git command git clone https://git.sr.ht/~pfm/gas.
  3. Enter the src subdirectory of the Gas project and start SBCL.
  4. Load the ASDF package: (require 'asdf).
  5. Load GAS using ASDF: (asdf:operate 'asdf:load-op 'gas).

At this point you can either:

6.1. Start GAS entering (gas-init:toplevel).

Or:

6.2. Prepare a Lisp image that won't require running the commands above by entering (gas-init:build t). This command will build an executable "gas.img" that you will be able to run instead of running SBCL.

#Basic Usage

GAS has a simple command interface. The most important command to remember is: HELP.

Other important commands include: LOAD (parses a FASTA or an ABIF file), M (matches two sequences against each other, finding common regions) and JOIN (interactively joins two sequences that were earlier matched).