search

legumeinfo / datastore-specifications

Specifications for directory naming, file naming, file contents in the LIS datastore
2 stars 0 forks source link

Specify /transcriptomes/ collections #4

Open sammyjava opened 3 years ago

sammyjava commented 3 years ago

https://legumeinfo.org/data/v2/Lupinus/albus/transcriptomes/

is an example. I don't load these into the mines, but a DS folder should have a spec here.

sammyjava commented 2 years ago 
Apios/americana/transcriptomes
└── LA2155.tcp.BTsx
    ├── apiam.LA2155.tcp1.BTsx.primary_Transcript.fna.gz
    ├── apiam.LA2155.tcp1.BTsx.reduced_by_Pv.tar.gz
    ├── apiam.LA2155.tcp1.BTsx.transcript_reduced.fna.gz
    ├── apiam.LA2155.tcp1.BTsx.transcript.fna.gz
    ├── apiam.LA2155.tcp1.BTsx.transdec_cds.fna.gz
    ├── apiam.LA2155.tcp1.BTsx.transdec_gene.gff3.gz
    ├── apiam.LA2155.tcp1.BTsx.transdec_gff3.bed.gz
    ├── apiam.LA2155.tcp1.BTsx.transdec_mRNA.fna.gz
    ├── apiam.LA2155.tcp1.BTsx.transdec_peptide.faa.gz
    ├── apiam.LA2155.tcp1.BTsx.transdec_pfam.dat.gz
    ├── CHANGES.LA2155.tcp.BTsx.txt
    ├── CHECKSUM.LA2155.tcp.BTsx.md5
    ├── MANIFEST.LA2155.tcp.BTsx.correspondence.yml
    ├── MANIFEST.LA2155.tcp.BTsx.descriptions.yml
    └── README.LA2155.tcp.BTsx.yml
Arachis/hypogaea/transcriptomes
└── Tifrunner.tcp1.sSQ6
    ├── Aradu_Araip_PBgeneID_to_BARgeneID.tsv.gz
    ├── arahy.Tifrunner.tcp1.sSQ6.mapped_to_A_genemodels.txt.gz
    ├── arahy.Tifrunner.tcp1.sSQ6.mapped_to_B_genemodels.txt.gz
    ├── arahy.Tifrunner.tcp1.sSQ6.transcript_atlas.fna.gz
    ├── CHANGES.Tifrunner.tcp1.sSQ6.txt
    ├── CHECKSUM.Tifrunner.tcp1.sSQ6.md5
    ├── MANIFEST.Tifrunner.tcp1.sSQ6.correspondence.yml
    ├── MANIFEST.Tifrunner.tcp1.sSQ6.descriptions.yml
    └── README.Tifrunner.tcp1.sSQ6.yml
Bauhinia/blakeana/transcriptomes
└── HK1.tcp1.CS40
    ├── baubl.HK1.tcp1.CS40.info_annot.gtf.gz
    ├── baubl.HK1.tcp1.CS40.transcript.fna.gz
    ├── baubl.HK1.tcp1.CS40.transcript.fna.gz.fai
    ├── baubl.HK1.tcp1.CS40.transcript.fna.gz.gzi
    ├── CHANGES.HK1.tcp1.CS40.txt
    ├── CHECKSUM.HK1.tcp1.CS40.md5
    ├── MANIFEST.HK1.tcp1.CS40.correspondence.yml
    ├── MANIFEST.HK1.tcp1.CS40.descriptions.yml
    ├── original_readme.txt
    └── README.HK1.tcp1.CS40.yml
Bauhinia/purpurea/transcriptomes
└── HK2.tcp1.KBWP
    ├── baupu.HK2.tcp1.KBWP.info_annot.gtf.gz
    ├── baupu.HK2.tcp1.KBWP.transcript.fna.gz
    ├── baupu.HK2.tcp1.KBWP.transcript.fna.gz.fai
    ├── baupu.HK2.tcp1.KBWP.transcript.fna.gz.gzi
    ├── CHANGES.HK2.tcp1.KBWP.txt
    ├── CHECKSUM.HK2.tcp1.KBWP.md5
    ├── MANIFEST.HK2.tcp1.KBWP.correspondence.yml
    ├── MANIFEST.HK2.tcp1.KBWP.descriptions.yml
    ├── original_readme.txt
    └── README.HK2.tcp1.KBWP.yml
Bauhinia/tomentosa/transcriptomes
└── HK3.tcp1.MSDG
    ├── bauto.HK3.tcp1.MSDG.transcript.fna.gz
    ├── bauto.HK3.tcp1.MSDG.transcript.fna.gz.fai
    ├── bauto.HK3.tcp1.MSDG.transcript.fna.gz.gzi
    ├── CHANGES.HK3.tcp1.MSDG.txt
    ├── CHECKSUM.HK3.tcp1.MSDG.md5
    ├── MANIFEST.HK3.tcp1.MSDG.correspondence.yml
    ├── MANIFEST.HK3.tcp1.MSDG.descriptions.yml
    ├── original_readme.txt
    └── README.HK3.tcp1.MSDG.yml
Bauhinia/variegata/transcriptomes
└── HK4.tcp1.NMSH
    ├── bauva.HK4.tcp1.NMSH.info_annot.gtf.gz
    ├── bauva.HK4.tcp1.NMSH.transcript.fna.gz
    ├── bauva.HK4.tcp1.NMSH.transcript.fna.gz.fai
    ├── bauva.HK4.tcp1.NMSH.transcript.fna.gz.gzi
    ├── CHANGES.HK4.tcp1.NMSH.txt
    ├── CHECKSUM.HK4.tcp1.NMSH.md5
    ├── MANIFEST.HK4.tcp1.NMSH.correspondence.yml
    ├── MANIFEST.HK4.tcp1.NMSH.descriptions.yml
    ├── original_readme.txt
    └── README.HK4.tcp1.NMSH.yml
Cajanus/cajan/transcriptomes
└── mixed.tcp1.mKS3
    ├── cajca.mixed.tcp1.mKS3.fna.gz
    ├── CHANGES.mixed.tcp1.mKS3.txt
    ├── CHECKSUM.mixed.tcp1.mKS3.md5
    ├── MANIFEST.mixed.tcp1.mKS3.correspondence.yml
    ├── MANIFEST.mixed.tcp1.mKS3.descriptions.yml
    ├── original_README.txt
    └── README.mixed.tcp1.mKS3.yml
Cercis/gigantea/transcriptomes
└── Sh1.tcp1.9YLH
    ├── cergi.Sh1.tcp1.9YLH.transcript.fna.gz
    ├── cergi.Sh1.tcp1.9YLH.transcript.fna.gz.fai
    ├── cergi.Sh1.tcp1.9YLH.transcript.fna.gz.gzi
    ├── CHANGES.Sh1.tcp1.9YLH.txt
    ├── CHECKSUM.Sh1.tcp1.9YLH.md5
    ├── MANIFEST.Sh1.tcp1.9YLH.correspondence.yml
    ├── MANIFEST.Sh1.tcp1.9YLH.descriptions.yml
    ├── original_readme.txt
    └── README.Sh1.tcp1.9YLH.yml
Lupinus/albus/transcriptomes
└── LAGI01.tcp1.6LMX
    ├── CHANGES.LAGI01.tcp1.6LMX.txt
    ├── CHECKSUM.LAGI01.tcp1.6LMX.md5
    ├── lupal.LAGI01.ann1.6LMX.txt.gz
    ├── lupal.LAGI01.tcp1.6LMX.fna.gz
    ├── MANIFEST.LAGI01.tcp1.6LMX.correspondence.yml
    ├── MANIFEST.LAGI01.tcp1.6LMX.descriptions.yml
    └── README.LAGI01.tcp1.6LMX.yml
Lupinus/angustifolius/transcriptomes
├── P27255.tcp1.ycvS
│   ├── CHANGES.P27255.tcp1.ycvS.txt
│   ├── CHECKSUM.P27255.tcp1.ycvS.md5
│   ├── lupan.P27255.tcp1.ycvS.Trinity.fna.gz
│   ├── MANIFEST.P27255.tcp1.ycvS.correspondence.yml
│   ├── MANIFEST.P27255.tcp1.ycvS.descriptions.yml
│   ├── original_readme.lupinexpress.txt
│   └── README.P27255.tcp1.ycvS.yml
├── Tanjil.tcp1.p27w
│   ├── CHANGES.Tanjil.tcp1.p27w.txt
│   ├── CHECKSUM.Tanjil.tcp1.p27w.md5
│   ├── lupan.Tanjil.tcp1.p27w.Trinity.fna.gz
│   ├── MANIFEST.Tanjil.tcp1.p27w.correspondence.yml
│   ├── MANIFEST.Tanjil.tcp1.p27w.descriptions.yml
│   ├── original_readme.lupinexpress.txt
│   └── README.Tanjil.tcp1.p27w.yml
└── Unicrop.tcp1.YVT4
    ├── CHANGES.Unicrop.tcp1.YVT4.txt
    ├── CHECKSUM.Unicrop.tcp1.YVT4.md5
    ├── lupan.Unicrop.tcp1.YVT4.Trinity.fna.gz
    ├── MANIFEST.Unicrop.tcp1.YVT4.correspondence.yml
    ├── MANIFEST.Unicrop.tcp1.YVT4.descriptions.yml
    ├── original_readme.lupinexpress.txt
    └── README.Unicrop.tcp1.YVT4.yml
Medicago/sativa/transcriptomes
└── mixed.tcp1.vRdj
    ├── CHANGES.mixed.tcp1.vRdj.txt
    ├── CHECKSUM.mixed.tcp1.vRdj.md5
    ├── MANIFEST.mixed.tcp1.vRdj.correspondence.yml
    ├── MANIFEST.mixed.tcp1.vRdj.descriptions.yml
    ├── medsa.mixed.tcp1.vRdj.Abyss.fna.gz
    ├── medsa.mixed.tcp1.vRdj.id_map.gz
    ├── medsa.mixed.tcp1.vRdj.stats.txt
    ├── original_README_lista_medsa-201202.txt
    └── README.mixed.tcp1.vRdj.yml
Zenia/insignis/transcriptomes
└── 162940.tcp1.WM01
    ├── CHANGES.162940.tcp1.WM01.txt
    ├── CHECKSUM.162940.tcp1.WM01.md5
    ├── MANIFEST.162940.tcp1.WM01.correspondence.yml
    ├── MANIFEST.162940.tcp1.WM01.descriptions.yml
    ├── README.162940.tcp1.WM01.yml
    └── zenin.162940.tcp1.WM01.fna.gz