---
file_transformation: 
perl -pe 's/^>/>glyma.Lee.gnm2.ann1./' Gma.cds.fa >glyma.Lee.gnm2.ann1.1FNT.cds.fna
perl -pe 's/^>/>glyma.Lee.gnm2.ann1./' Gma.pep.fa >glyma.Lee.gnm2.ann1.1FNT.protein.faa
perl -pe 's/^>/>glyma.Lee.gnm2.ann1./' Gma.longestmRNA.pep.fa >glyma.Lee.gnm2.ann1.1FNT.protein_primary.faa
perl -pe 's/^>/>glyma.Lee.gnm2.ann1./' Gma.longestmRNA.cds.fa >glyma.Lee.gnm2.ann1.1FNT.cds_primary.fna
perl -pe 's/^Gm.Lee_(\S+)_v2.0/glyma.Lee.gnm2.$1/; s/ID=/ID=glyma.Lee.gnm2.ann1./; s/Parent=/Parent=glyma.Lee.gnm2.ann1./' Gma.genes.gff |perl -pe 'if ($_=~ /mRNA/){s/ID=(\S+)(;.+Name=).+/ID=$1$2$1/}' >glyma.Lee.gnm2.ann1.1FNT.gene_models_main.gff3
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changes:
  - 2022-02-25 initial Legume Federation Data Store file preparation
  - 2022-02-25 Applied prefixes to fasta and GFF files - see file_transformations above
  - 2022-03-05 Add AHRD annotation and gene family assignments
  - 2022-03-23 remove .Lee_v2.0 with perl -pe 's/.Lee_v2.0//g' in cds, protein fasta files; gene_models_main and iprscan gff3 files; and gfa.tsv file.
  - 2022-04-05 adf: added mrna files produced by gffread
  - 2024-04-11 sbc: update synopsis to include JGI numbering