---
file_transformation: 
perl -pe 's/HIC_ASM_0/Chr01/; s/HIC_ASM_1\t/Chr02\t/; s/HIC_ASM_2/Chr03/; s/HIC_ASM_3/Chr04/; s/HIC_ASM_4/Chr05/; s/HIC_ASM_5/Chr06/; s/HIC_ASM_6/Chr07/; s/HIC_ASM_7/Chr08/; s/HIC_ASM_8/Chr09/; s/HIC_ASM_9/Chr10/; s/HIC_ASM_10/Chr11/; s/HIC_ASM_11/Chr12/' pasa2.longest.filter.gff3  > pasa2.longest.filter_chr.gff3

perl -pe 's/^/singl.CAF01.gnm1./; s/ID=/ID=singl.CAF01.gnm1.ann1./; s/Parent=/Parent=singl.CAF01.gnm1.ann1./' pasa2.longest.filter_chr.gff3 >singl.CAF01.gnm1.ann1.WFKC.gene_model_main.gff3

cat JAIUCU01.fna |perl -pe 's/>.+glabra (\S+),.+/>$1/; s/>.+glabra (\S+) (\d),.+/>Chr0$2/; s/>.+glabra (\S+) (\d\d),.+/>Chr$2/' >JAIUCU01.chromosomeID.fna
gffread -x JAIUCU01_cds.fna -g JAIUCU01.chromosomeID.fna pasa2.longest.filter_chr.gff3
gffread -y JAIUCU01_protein.faa -g JAIUCU01.chromosomeID.fna pasa2.longest.filter_chr.gff3

changes:
  - 2022-04-18 initial Legume Federation Data Store file preparation
  - Applied prefixes to fasta and GFF files - see file_transformations above

  - 2022-06-26 SCannon: patch IDs in cds, protein, and gff files:
  for filepath in BAK/*.f?a; do
    filename=`basename $filepath`
    echo $filename
    cat $filepath |
      perl -pe 's/evm.model./evm_model_/g' |
      perl -pe 's/HIC_ASM_0\./Chr01_/g; s/HIC_ASM_1\./Chr02_/g; s/HIC_ASM_2\./Chr03_/g;  s/HIC_ASM_3\./Chr04_/g; ' |
      perl -pe 's/HIC_ASM_4\./Chr05_/g; s/HIC_ASM_5\./Chr06_/g; s/HIC_ASM_6\./Chr07_/g;  s/HIC_ASM_7\./Chr08_/g; ' |
      perl -pe 's/HIC_ASM_8\./Chr09_/g; s/HIC_ASM_9\./Chr10_/g; s/HIC_ASM_10\./Chr11_/g; s/HIC_ASM_11\./Chr12_/g; ' |
      perl -pe 's/(\d)\.(\d+)$/$1_$2/g; s/_(\d+)\.(\d+)_/_$1_$2_/' > $filename
  done

  for filepath in BAK/*.gff3; do
    filename=`basename $filepath`
    echo $filename
    cat $filepath |
      perl -pe 's/evm\.TU\./evm_TU_/g; s/cds\.evm\.model\./cds_evm_model_/g; s/evm\.model\./evm_model_/g;' |
      perl -pe 's/HIC_ASM_0\./Chr01_/g; s/HIC_ASM_1\./Chr02_/g; s/HIC_ASM_2\./Chr03_/g;  s/HIC_ASM_3\./Chr04_/g; ' |
      perl -pe 's/HIC_ASM_4\./Chr05_/g; s/HIC_ASM_5\./Chr06_/g; s/HIC_ASM_6\./Chr07_/g;  s/HIC_ASM_7\./Chr08_/g; ' |
      perl -pe 's/HIC_ASM_8\./Chr09_/g; s/HIC_ASM_9\./Chr10_/g; s/HIC_ASM_10\./Chr11_/g; s/HIC_ASM_11\./Chr12_/g; ' |
      perl -pe 's/(\d)\.(\d+)$/$1_$2/g; s/(\d)\.(\d+);/$1_$2;/g; s/_(\d+)\.(\d+)_/_$1_$2_/' |
      perl -pe 's/%3A%20/__/g; s/%3B%20/__/g' > $filename
  done

  - 2023-08-31: Removed the following bad gene models:
singl.CAF01.gnm1.ann1.evm_model_CTG_1044_1_1
singl.CAF01.gnm1.ann1.evm_model_CTG_1301_1_evm_model_CTG_1301_2
singl.CAF01.gnm1.ann1.evm_model_CTG_519_4_1
singl.CAF01.gnm1.ann1.evm_model_CTG_107_9_1
singl.CAF01.gnm1.ann1.evm_model_CTG_399_1_4
singl.CAF01.gnm1.ann1.evm_model_CTG_547_6_1
singl.CAF01.gnm1.ann1.evm_model_CTG_31_1_1
singl.CAF01.gnm1.ann1.evm_model_CTG_443_1_1
singl.CAF01.gnm1.ann1.evm_model_CTG_1043_3_evm_model_CTG_1043_4
singl.CAF01.gnm1.ann1.evm_model_CTG_458_1_1
singl.CAF01.gnm1.ann1.evm_model_CTG_251_1_4_evm_model_CTG_251_1_5
singl.CAF01.gnm1.ann1.evm_model_CTG_914_3_3
singl.CAF01.gnm1.ann1.evm_model_CTG_440_1_1
singl.CAF01.gnm1.ann1.evm_model_CTG_1417_3_1
singl.CAF01.gnm1.ann1.evm_model_CTG_36_2_evm_model_CTG_36_3
singl.CAF01.gnm1.ann1.evm_model_CTG_513_2_evm_model_CTG_513_4
singl.CAF01.gnm1.ann1.evm_model_CTG_1241_2_1
singl.CAF01.gnm1.ann1.evm_model_CTG_549_1_evm_model_CTG_549_2
singl.CAF01.gnm1.ann1.evm_model_CTG_1073_3_3
singl.CAF01.gnm1.ann1.evm_model_CTG_1073_8_4
singl.CAF01.gnm1.ann1.evm_model_CTG_548_5_1
singl.CAF01.gnm1.ann1.evm_model_CTG_20_8_1
singl.CAF01.gnm1.ann1.evm_model_CTG_932_2_15
singl.CAF01.gnm1.ann1.evm_model_CTG_932_3_15
singl.CAF01.gnm1.ann1.evm_model_CTG_499_1_1
singl.CAF01.gnm1.ann1.evm_model_CTG_501_4_2
singl.CAF01.gnm1.ann1.evm_model_CTG_501_6_1
singl.CAF01.gnm1.ann1.evm_model_CTG_1011_7_3