---
file_transformation: 
  - Prefixed gene IDs with glyma.Wm82.gnm2.ann1. in glyma.Wm82.gnm2.ann1.RVB6.gene_models_main.gff3  
  - Prefixed fasta files with glyma.Wm82.gnm2. and removed .p suffix:
    - do perl -pi -e 's/>(\S+)\.p />glyma.Wm82.gnm2.$1 /' *.faa
  - Added chromosome prefix to GFFs:
    - perl -pi -e 's/^Chr(\d+)/glyma.Wm82.gnm2.Gm$1/; s/^(scaffold_\d+)/glyma.Wm82.gnm2.$1/' glyma.Wm82.gnm2.ann1.RVB6.gene.gff3
    - perl -pi -e 's/^Chr(\d+)/glyma.Wm82.gnm2.Gm$1/; s/^(scaffold_\d+)/glyma.Wm82.gnm2.$1/' glyma.Wm82.gnm2.ann1.RVB6.repeatmasked_assembly_v2.0.gff3
  - Prefixed gene IDs in nucleotide fasta:
    - perl -pi -e 's/>(\S+) />glyma.Wm82.gnm2.$1 /' *fna

changes: 
  - 2018-02-28 prefixed gene IDs with glyma.Wm82.gnm2.ann1. in gene_models_main.gff3
  - 2018-03-01 pulled file lists into MANIFEST files
  - 2018-03-01 rm glyma.Wm82.gnm2.ann1.RVB6.gene_exons.gff3.gz
  - 2018-03-01 filename cleanup
  - 2018-07-05 added annotation file glyma.Wm82.gnm2.ann1.RVB6.info_gene_annot.txt, derived from GFF
  - 2018-08-16 Added "glyma.Wm82.gnm2." prefixes to fasta files and removed ".p" suffix from .faa files
  - 2018-09-15 Fixed prefixing to glyma.Wm82.gnm2.ann1.
  - 2020-09-22 added gene family assignments
  - 2021-05-25 updated gene family assignments to use score rather than e-value 
  - 2022-01-23 removed spurious Wm82.a2.v1 parts from GFF identifiers (SH)
  - 2024-04-11 sbc: update synopsis to include JGI numbering