---
file_transformation: 
  - Modifications were made to the GFF for display in GBrowse. File for display was titled
  - Lupinus_ang_Tanjil.a1.v1.genes_in_pchr_acaffs_ge10k.final.gff3 . Modifications as follows (Wei Huang and Steven Cannon):
  - Due to some features lacking primary_id, gene, We need to work on the gff file before upload,
  - Lup002418 add gene and mRNA features,
  - Lup006306 deleted; bad prediction: no hits in other predicted legume genes. No gene feature in gff.
  -   
  - Lup018375 deleted; bad prediction (93-base repeat). Strike from sequence files.
  - Lup021820 deleted; bad (gappy) prediction. Strike from sequence files.
  - Lup012883  Bad prediction (CDS only; gappy gene prediction). Strike from CDS and peptide files
  - Added the following to lupan.Tanjil.gnm1.ann1.nnV9.genes_pchr_plus_scaff.gff3:
  - Lup008273, Lup002418
  - perl -pi -e 's/ +/\t/g if 229259' Lupinus_ang_Tanjil.a1.v1.genes_in_pchr_acaffs_ge10k.modified.gff3 
  - perl -pi -e 's/ +/\t/g if 229260' Lupinus_ang_Tanjil.a1.v1.genes_in_pchr_acaffs_ge10k.modified.gff3                        
  - cat Lupinus_ang_Tanjil.a1.v1.genes_in_pchr_acaffs_ge10k.modified.gff3 |
  - perl -ne 'if (/gene/ && /source_id/) {s/(ID=Lup\d+)\.\d/$1/;
  - s/(Name=Lup\d+)\.\d/$1/;print;}elsif (/mRNA/ && /source_id/){s/(Parent=Lup\d+)\.\d/$1/;print;}else {print}'
  - >Lupinus_ang_Tanjil.a1.v1.genes_in_pchr_acaffs_ge10k.final.gff3
  - Lupinus_ang_Tanjil.a1.v1.genes_in_pchr_acaffs_ge10k.final.gff3 was then renamed to 
  - lupan.Tanjil.gnm1.ann1.nnV9.genes_in_pchr_plus_scaff_ge10k.gff3

changes: 
  - 2018-03-01 pulled file lists into MANIFESTS
  - 2018-03-01 filename cleanup
  - 2018-09-15 fasta header changes (s/>/>lupan.Tanjil.gnm1.ann1./)
  - 2020-09-25 added gene family assignments
  - 2021-07-02 added ID attributes to features without them (fixes https://github.com/legumeinfo/datastore-issues/issues/29)
  - 2021-07-29 adf: added transcript file derived from gffread (fixes https://github.com/legumeinfo/datastore-issues/issues/50); removed lupan.Tanjil.gnm1.ann1.nnV9.cds_all.fna.gz which was the same as lupan.Tanjil.gnm1.ann1.nnV9.cds.fna.gz