---
directories:
    work_dir: /usr/local/www/data/private/Cercis/canadensis
    from_annot_dir: ISC453364.gnm3_hap2.ann1/V3.1/annotation
    from_genome_dir: ISC453364.gnm3_hap2.ann1/V3.1/assembly
prefixes:
    from_annot_prefix: "CcanadensisHAP2_706_V3.1."
    from_genome_prefix: "CcanadensisHAP2_706_V3.0."
# Some preprocessing:
# The GFF features all include ".V3.1", e.g. Cecan.1G000100.V3.1  or  Cecan.1G000100.1.V3.1.CDS.1
# but the fasta files do not, e.g. Cecan.1G000100.1 
# Fix this inconsistency by removing .V3.1 from the GFFs: 's/\.V3\.1//g'

collection_info:
    genus: Cercis
    species: canadensis
    scientific_name_abbrev: cerca
    coll_genotype: ISC453364
    gnm_ver: gnm3_hap2
    ann_ver: ann1
    genome_key: 2S7P
    annot_key: G88H
readme_info:
    provenance: "The files in this directory originated from http://phytozome.jgi.doe.gov. The Phytozome repository is considered the primary repository and authoritative; files in this present directory are derived, and may have changes, as noted below. The files here are held as part of the LegumeInfo and SoyBase projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the LegumeInfo and SoyBase projects. If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please respect any usage restrictions in the present and original repositories, and cite the data appropriately."
    source: "https://phytozome-next.jgi.doe.gov/info/GmaxWm82ISU_01_v2_1"
    synopsis_genome: Cercis canadensis accession ISC453364, genome assembly v3 haplotype 2
    synopsis_annot: Annotation 1 for Cercis canadensis accession ISC453364, genome assembly v3 haplotype 2
    genotype: ISC453364
    taxid: "49801"
    description_genome: "This release is from a tree on the Iowa State University campus, registered as accession ISC453364. The resulting genome assembly was resolved into two haplotype assemblies. This particular assembly has been designated as haplotype 1. For full description of assembly methods and characteristics, see the Phytozome description at the URL above."
    chromosome_prefix: chr
    supercontig_prefix: scaffold
    description_annot: "Gene annotation resources. See full description at Phytozome/JGI repository (address above)."
    bioproject: 
    sraproject: 
    dataset_doi_genome: 
    dataset_doi_annot: 
    genbank_accession: 
    original_file_creation_date: 2023-03-08
    local_file_creation_date: 2024-07-15
    dataset_release_date: 2023-08-01
    contributors: Steven Cannon, Jim Leebens-Mack, Jacob Stai, Jeremy Schmutz
    publication_doi: 
    citation: "Lee H, Stai JS, ... Leebens-Mack, Cannon SB. Analysis of new reference genome assemblies for Cercis canadensis and Chamaecrista fasciculata clarify evolutionary histories of legume nodulation and genome structure (in preparation)"
    publication_title: 
    data_curators: Steven Cannon
    public_access_level: public, restricted
    license: Open, with usage agreement
    keywords: "redbud, Cercis canadensis"
from_to_genome:
  - 
    from: fa.gz
    to: genome_main.fna
    description: "Primary genome assembly"
  - 
    from: hardmasked.fa.gz
    to: genome_hardmasked.fna
    description: "Genome assembly - softmasked"
  - 
    from: softmasked.fa.gz
    to: genome_softmasked.fna
    description: "Genome assembly - hardmasked"
original_readme_and_usage:
  - 
    from_full_filename: CcanadensisHAP2_706_V3.1.DataReleasePolicy.html
    to: DataReleasePolicy.html
    description: "Original JGI data release policy"
  - 
    from_full_filename: CcanadensisHAP2_706_V3.1.readme.txt
    to: original_readme.txt
    description: "Original JGI data README file"
from_to_annot_as_is:
  - 
    from: repeatmasked_assembly_V3.0.gff3.gz
    to: repeatmasked_assembly.gff3
    description: "GFF with repeat-masking coordinates"
  - 
    from: annotation_info.txt.gz
    to: annotation_info.txt
    description: "Table of gene annotations from JGI"
  - 
    from: defline.txt.gz
    to: defline.txt
    description: "Defline for genes from JGI"
from_to_genome_as_is:
from_to_cds_mrna:
  - 
    from: cds.fa.gz
    to: cds.fna
    description: "cds sequences"
  - 
    from: cds_primaryTranscriptOnly.fa.gz
    to: cds_primary.fna
    description: "cds sequences - primary only"
  - 
    from: transcript.fa.gz
    to: mrna.fna
    description: "Transcript sequences"
  - 
    from: transcript_primaryTranscriptOnly.fa.gz
    to: mrna_primary.fna
    description: "Transcript sequences - primary only"
from_to_protein:
  - 
    from: protein_primaryTranscriptOnly.fa.gz
    to: protein_primary.faa
    strip: '\.p'
    description: "Protein sequences - primary only"
  - 
    from: protein.fa.gz
    to: protein.faa
    strip: '\.p'
    description: "Protein sequences"
from_to_gff:
## Skip gene_exons because a featid_map isn't generated by default for exon features.
#  - 
#    from: gene_exons_strip.gff3.gz
#    to: gene_models_exons.gff3
#    description: "Gene models, with exon features"
  - 
    from: gene_strip.gff3.gz
    to: gene_models_main.gff3
    description: "Gene models - main"