This repository contains the code for my masters project par in its initial form, written in literate programming style. For a more recent version I split this in two. The library for indexing the input and for matching can be found at github.com/dadidange/esaMatcher. Currently, I am working on some adaptions at the code to compute the alignments. At some point, this will be published at github.com/dadidange/par.
Right now, this repository here should work best.
To run it from scratch type make
.
This will overwrite most of the files.
For this to work, some dependencies need to be installed:
- noweb
$ sudo apt install noweb
- latex
- go
- libdivsufsort
$ sudo apt install libdivsufsort-dev
The working directory should now contain the executable par and the corresponding code in src.
The directory ./texfiles contains the document pardoc.pdf
for documentation.
The documentation is rather a monologue that needs to be reworked.
Running from scratch is not necessary, code and documentation are already provided.
To just compile the code, type go build
in the src/par
directory.
libdivsufsort and go are still required for this.
Par expects FASTA files as input. For example, it can be applied to the 4 covid genomes in ./samples/.
./par samples/*.fa > covid.maf
Results in a multiple alignment in MAF-format.
mview is a great tool to display alignments a little better than plain text. Mview is available here: https://github.com/desmid/mview/ and could be executed like this:
mview -in maf -html head -css on -coloring mismatch covid.maf > covid.html