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legumeinfo / datastore-specifications

Specifications for directory naming, file naming, file contents in the LIS datastore
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Move /maps/ directories to /genetic/ #8

Closed sammyjava closed 2 years ago

sammyjava commented 2 years ago
sammyjava commented 2 years ago

@cann0010 can Arachis/hypogaea/maps/ be deleted or moved elsewhere? It appears to me that they've all been converted to v2 collections under /genetic/ (probably by me) and we don't have /maps/ collections in the spec. I think they're just left from v1.

[shokin@lis-stage ~/v2/Arachis/hypogaea]$ ls -1 maps/
TT_AhComposite_SujayGowda2012.map.9G9T
TT_AhConsensus_GautamiPandey2012.map.DBF1
TT_Huayu28_x_P76.map.WBH8
TT_ICGS44_x_ICGS76.map.LD1X
TT_ICGS76_x_CSMG84.map.VRNN
TT_TAG24_x_GPBD4.map.L0CZ
TT_TAG24_x_ICGV86031.map.BYVP
TT_TG26_x_GPBD4_a.map.VB8Z
TT_TG26_x_GPBD4_b.map.PPD3
TT_Tifrunner_x_GT-C20_b.map.R59G
TT_Tifrunner_x_GT-C20_c.map.Z2ST
TT_VG9514_x_TAG24.map.C78H

[shokin@lis-stage ~/v2/Arachis/hypogaea]$ ls -1 genetic/
Huayu28_x_P76.gen.Hu_Zhang_2018
ICGS44_x_ICGS76.gen.Gautami_Pandey_2012
ICGS76_x_CSMG84.gen.Gautami_Pandey_2012
mixed.gen.Gautami_Pandey_2012
mixed.gen.Sujay_Gowda_2012
NAMFlor7.gwas.Gangurde_Wang_2020
NAMTifr.gwas.Gangurde_Wang_2020
SunOleic97R_x_NC94022.gen.Qin_Feng_2012
TAG24_x_GPBD4.gen.Kolekar_Sujay_2016
TAG24_x_ICGV86031.gen.Ravi_Vadez_2011
TG26_x_GPBD4.gen.Sarvamanga_Gowdaa_2011
TG26_x_GPBD4.gen.Sujay_Gowda_2012
Tifrunner_x_GT-C20.gen.Agarwal_Clevenger_2018
Tifrunner_x_GT-C20.gen.Qin_Feng_2012
Tifrunner_x_GT-C20.gen.Wang_Penmetsa_2012
USPeanutCore.gwas.Otyama_Kulkarni_2020
VG9514_x_TAG24.gen.Mondal_Hadapad_2014
StevenCannon-USDA commented 2 years ago

Checking these now ...

StevenCannon-USDA commented 2 years ago

I agree: the contents of "maps" are present in "genetic". The "maps" directory is a legacy from v1. I have removed that directory from v2. If the legacy (v1) content is needed, it can be found at /usr/local/www/data/v1/Arachis_hypogaea/ In the v1 directory, I have converted the hard-linked directories into stand-alone, unlinked directories. Mention to @sdash-github, in case links need to be created to this content in "peanutbase-next". Here are the correspondences (I verified these by checking line counts in the cmap files; I didn't check other differences such as in the READMEs - which are expected and intentional).

genetic (v2) maps (v1)
Huayu28_x_P76.gen.Hu_Zhang_2018 TT_Huayu28_x_P76.map.WBH8
ICGS44_x_ICGS76.gen.Gautami_Pandey_2012 TT_ICGS44_x_ICGS76.map.LD1X
ICGS76_x_CSMG84.gen.Gautami_Pandey_2012 TT_ICGS76_x_CSMG84.map.VRNN
mixed.gen.Gautami_Pandey_2012 TT_AhConsensus_GautamiPandey2012.map.DBF1
mixed.gen.Sujay_Gowda_2012 TT_AhComposite_SujayGowda2012.map.9G9T
NAMFlor7.gwas.Gangurde_Wang_2020  
NAMTifr.gwas.Gangurde_Wang_2020  
SunOleic97R_x_NC94022.gen.Qin_Feng_2012  
TAG24_x_GPBD4.gen.Kolekar_Sujay_2016 TT_TAG24_x_GPBD4.map.L0CZ
TAG24_x_ICGV86031.gen.Ravi_Vadez_2011 TT_TAG24_x_ICGV86031.map.BYVP
TG26_x_GPBD4.gen.Sarvamanga_Gowdaa_2011 TT_TG26_x_GPBD4_b.map.PPD3
TG26_x_GPBD4.gen.Sujay_Gowda_2012 TT_TG26_x_GPBD4_a.map.VB8Z
Tifrunner_x_GT-C20.gen.Agarwal_Clevenger_2018 TT_Tifrunner_x_GT-C20_c.map.Z2ST
Tifrunner_x_GT-C20.gen.Qin_Feng_2012  
Tifrunner_x_GT-C20.gen.Wang_Penmetsa_2012 TT_Tifrunner_x_GT-C20_b.map.R59G
USPeanutCore.gwas.Otyama_Kulkarni_2020  
VG9514_x_TAG24.gen.Mondal_Hadapad_2014 TT_VG9514_x_TAG24.map.C78H