This is a script which generates a fragment recruitment plot.
ASSUMPTIONS: It is assumed that the file format will be in the SAM or PSL format, with the extensions limited to .sam or .psl. It is assumed that there will be three input samples each run. To run just one or two samples, input the same sample multiple times. It is assumed that the input samples will have been aligned to the same Reference Genome, as the Ref. Genome name printed in the plotter will only display the ref genome from the last input sample. Due to the small scope of this project, it is assumed that .sam files were aligned via Bowtie2 and .psl files were aligned via FR-HIT.
The aligned reads have been named with a specific protocol as follows: abau_4e.sam, aodo_is.psl, etc. If this format is followed, this program parses the input names to generate the legend labels and the graph reference genome name. If this format is not followed, the graph will still be generated, however, the aforementioned labels will revert to 'unknown' in the generated graphic.
Only the 10 reference genomes pertinent to this project are automatically parsed and displayed as their full scientific name.