Dr. Muday asked for the SL4 gene names to be their own column with the description. So I made an R script and created an output file with the columns "SL4, SL5, Description". I also just added the new SL4 column to the original counts file.
Script:
SL4_SL5_Description.R
File with just gene names and description:
SL4_SL5_description_tomato.csv
File with SL4 column added on to the end of original counts file:
SL4_SL5_counts_muday-144.csv

Reviewer:

• Please check code for any running errors or output errors. Also if I need to clean anything up!
• Check the output files and see if the structure is correct and makes sense based on Dr. Muday's request.
  Thank you!

Possible improvements:

• Modify "AddGeneAnnotations.Rmd" so that it adds a new column "SL4_gene_id"

Possible benefit of above: Fewer files to track

References / Documentation:

• https://bitbucket.org/hotpollen/splicing-analysis/src/main/DescriptionMapping/

This makes gene descriptions, using input from SL4_SL5_description.R.

Possible improvement:

• Modify the "DescriptionMapping" code to create SL4_SL5_description_tomato.csv (new file)
• Make new repo to capture just the description mapping code, and make it a "product" for bioinformatics researchers like us

Re-reading above, I realized that my previous comments sounded too much like commands for my taste, and not enough like suggestions. I revised them.