legumeinfo / datastore-specifications

Specifications for directory naming, file naming, file contents in the LIS datastore
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mismatch between synteny spec and actual practice? #34

Closed adf-ncgr closed 1 year ago

adf-ncgr commented 1 year ago

While trying to cop the synteny spec for use in the genome_alignments context, I noticed that the spec doesn't include keys in the file names whereas they seem to be included in datastore files. e.g.: spec sez: Example:

IT97K-499-35.gnm1.syn.W3NY
├── vigun.IT97K-499-35.gnm1.x.glyma.Wm82.gnm2.gff.gz
├── vigun.IT97K-499-35.gnm1.x.phavu.G19833.gnm1.gff.gz
├── vigun.IT97K-499-35.gnm1.x.vigan.Gyeongwon.gnm3.gff.gz
├── vigun.IT97K-499-35.gnm1.x.vigra.VC1973A.gnm6.gff.gz
└── vigun.IT97K-499-35.gnm1.x.vigun.IT97K-499-35.gnm1.gff.gz

while datastore has: [adf@lis-stage /usr/local/www/data/v2/Vigna/unguiculata/synteny/IT97K-499-35.gnm1.syn.W3NY]$ ls README.IT97K-499-35.gnm1.syn.W3NY.yml vigun.IT97K-499-35.gnm1.x.glyma.Wm82.gnm2.W3NY.gff3.gz vigun.IT97K-499-35.gnm1.x.phavu.G19833.gnm1.W3NY.gff3.gz vigun.IT97K-499-35.gnm1.x.vigan.Gyeongwon.gnm3.W3NY.gff3.gz vigun.IT97K-499-35.gnm1.x.vigra.VC1973A.gnm6.W3NY.gff3.gz vigun.IT97K-499-35.gnm1.x.vigun.IT97K-499-35.gnm1.W3NY.gff3.gz

I'm guessing the latter is considered correct, but will defer to the keymasters.

StevenCannon-USDA commented 1 year ago

Yeah, I think "the latter is considered correct", following the general pattern that files include the key.

sammyjava commented 1 year ago

I updated the spec.