---
file_transformation: 
changes: Begin each change note with a date string, e.g. 2018-03-23 -->

  - 2018-05-08 Changed gff column 1 IDs from CcLG to cajca.ICPL87119.gnm1.Cc
  - 2018-07-12 2018-07-11 Changed fasta header in all *.fna and *.faa files (perl -pi -e 's/>Aradu/>aradu.V14167.gnm1.ann1/')
  - 2018-09-15 Changed fasta header in all *.fna and *.faa files to include .1 suffixes and amend the above to match the gff3 (e.g. C.cajan had been removed)
  - 2019-08-28 Tweak GFF for compliance - changing "nan" in 6th field to "."
  - 2020-09-22 added gene family assignments file
  - 2021-07-26 adf: added ID attributes via add_IDs_to_gff_features.pl (fixes https://github.com/legumeinfo/mine-issues/issues/38)
  - 2021-07-27 adf: gffread creation of transcript.fna; fixed naming of protein.faa (was protein_main.faa)
  - 2021-07-28 adf: added cajca.ICPL87119.gnm1.ann1.Y27M.pathway.tsv derived from Plant Reactome
  - 2022-01-20 scannon: renamed sequence files to bring them in line with Data Store patterns:
      rm cajca.ICPL87119.gnm1.ann1.Y27M.mrna.fna.gz   because it is the same as cajca.ICPL87119.gnm1.ann1.Y27M.cds.fna.gz
       and seems to be CDS rather than mrna sequence
      mv cajca.ICPL87119.gnm1.ann1.Y27M.protein.faa.gz cajca.ICPL87119.gnm1.ann1.Y27M.protein_with_TEs.faa.gz
      mv cajca.ICPL87119.gnm1.ann1.Y27M.gene_main.fna.gz cajca.ICPL87119.gnm1.ann1.Y27M.gene_main.fna.gz
      mv cajca.ICPL87119.gnm1.ann1.Y27M.gene_filterTE.fna.gz cajca.ICPL87119.gnm1.ann1.Y27M.mrna.fna.gz
      mv cajca.ICPL87119.gnm1.ann1.Y27M.gene_main.fna.gz cajca.ICPL87119.gnm1.ann1.Y27M.mrna_with_TEs.fna.gz
      mv cajca.ICPL87119.gnm1.ann1.Y27M.protein_filterTE.faa.gz cajca.ICPL87119.gnm1.ann1.Y27M.protein.faa.gz
    The resulting sequence counts:
    zgrep -c '>' *.f?a.gz
      cajca.ICPL87119.gnm1.ann1.Y27M.cds.fna.gz:40071
      cajca.ICPL87119.gnm1.ann1.Y27M.mrna_with_TEs.fna.gz:48680
      cajca.ICPL87119.gnm1.ann1.Y27M.mrna.fna.gz:40071
      cajca.ICPL87119.gnm1.ann1.Y27M.protein_with_TEs.faa.gz:48680
      cajca.ICPL87119.gnm1.ann1.Y27M.protein.faa.gz:40071
 - 2022-03-05 adf: reran gene family assignment since older one included content no longer found in gene_models_main