---
directories:
    work_dir: /usr/local/www/data/private/Medicago/GENUS
    from_pan_dir: out_Medicago_7_16
prefixes:
    from_pan_prefix: 
collection_info:
    genus: Medicago
    pan_ver: pan1
    pan_key: XXQ6
readme_info:
    provenance: "The files in this directory are a product of the staff of the SoyBase and LegumeInfo project teams. The method is described here: https://github.com/legumeinfo/pandagma"
    source: "https://data.legumeinfo.org"
    synopsis: "Pangene set for Medicago species, based primarily on M. truncatula but also including M. sativa. This pangene set includes 19 annotation sets."
    taxid: "3877"
    annotations_main: medsa.XinJiangDaYe_1.gnm1.ann1,medsa.XinJiangDaYe_2.gnm1.ann1,medsa.XinJiangDaYe_3.gnm1.ann1,medsa.XinJiangDaYe_4.gnm1.ann1,medtr.A17_HM341.gnm4.ann2,medtr.A17.gnm5.ann1_6,medtr.R108.gnmHiC_1.ann1
    annotations_extra: medsa.XinJiangDaYe_sc.gnm1.ann1,medtr.HM004.gnm1.ann1,medtr.HM010.gnm1.ann1,medtr.HM022.gnm1.ann1,medtr.HM023.gnm1.ann1,medtr.HM034.gnm1.ann1,medtr.HM050.gnm1.ann1,medtr.HM056.gnm1.ann1,medtr.HM058.gnm1.ann1,medtr.HM060.gnm1.ann1,medtr.HM095.gnm1.ann1,medtr.HM125.gnm1.ann1,medtr.HM129.gnm1.ann1,medtr.HM185.gnm1.ann1,medtr.HM324.gnm1.ann1,medtr.R108_HM340.gnm1.ann1
    description: "Pan-gene set for Medicago species, spanning 2 species and 19 annotation sets, calculated using the pandagma pipeline, version 2023-04-03"
    bioproject: 
    sraproject: 
    dataset_doi_genome: 
    dataset_doi_annot: 
    genbank_accession: 
    original_file_creation_date: 2023-04-03
    local_file_creation_date: 2023-04-03
    dataset_release_date: 2023-04-03
    contributors: Steven Cannon, Hyunoh Lee
    publication_doi: 
    citation: 
    publication_title: 
    data_curators: Steven Cannon
    public_access_level: public
    license: Open
    keywords: "Medicago, barrel medic, alfalfa, lucerne, pan-gene, pangene, orthogroup"
from_to_pan_tsv:
  - 
    from: 18_syn_pan_aug_extra.clust.tsv
    to: clust.tsv
    description: "Pan-gene sets, in cluster format: ID in first column, followed by tab-separated gene list."
  - 
    from: 18_syn_pan_aug_extra.counts.tsv
    to: counts.tsv
    description: "Matrix of counts of genes per annotation set for each pan-gene set."
  - 
    from: 18_syn_pan_aug_extra.hsh.tsv
    to: hsh.tsv
    description: "Pan-gene sets, in a two-column hash format, with the set ID in the first column and genes in the second."
from_to_pan_fasta:
  - 
    from: 21_pan_fasta_clust_rep_cds.fna
    to: inclusive_cds.fna
    description: "CDS pan-gene sequence, inclusive (not filtered by minimum cluster size or annotation-set representation)."
  - 
    from: 21_pan_fasta_clust_rep_prot.faa
    to: inclusive_protein.faa
    description: "Protein pan-gene sequence, inclusive (not filtered by minimum cluster size or annotation-set representation)."
  - 
    from: 23_syn_pan_pctl25_posn_cds.fna
    to: pctl25_named_cds.fna
    strip: '\w+\.pan\d+\.'
    description: "CDS pan-gene sequence, omitting pan-genes smaller than 25% of the mode, with derived pan-gene IDs corresponding with consensus chromosome and ordinal position."
  - 
    from: 23_syn_pan_pctl25_posn_prot.faa
    to: pctl25_named_protein.faa
    strip: '\w+\.pan\d+\.'
    description: "Protein pan-gene sequence, omitting pan-genes smaller than 25% of the mode, with derived pan-gene IDs corresponding with consensus chromosome and ordinal position."
from_to_pan_as_is:
  - 
    from: 18_syn_pan_aug_extra_complement.fna
    to: complement.fna
    description: "Complement of genes in this pan-gene set; i.e. not clustered, presumed to be singletons."
  - 
    from: stats.Medicago_7_16.txt
    to: stats.txt
    description: "Descriptive statistics about program parameters, input sequences, and pan-gene products."