img_scripts
A collection of scripts dealing with local stores of IMG data.
img_metadata_scanner.rb
Scan through a taxon metadata file, filtering by particular fields. Only certain fields are extracted.
Print out the genus and species of each archaeon:
$ img_metadata_scanner.rb Domain=Archaea --output-fields "Genus,Species" |head
Thermococcus gammatolerans
Methanolobus
Pyrobaculum
Methanobacterium sp.
Sulfolobus islandicus
Desulfurococcus mucosus
Haladaptatus paucihalophilus
Methanothermobacter thermautotrophicus
Methanosarcina barkeri
Methanobrevibacter smithiiPrint out the headers available for filtering or reporting
$ img_metadata_scanner.rb -l |less
taxon_oid
Domain
Status
Proposal Name
etc.
etc.Randomly sample each species in the genus Shigella:
$ img_metadata_scanner.rb --output-fields "taxon_oid,Genus,Species" Genus=Shigella --sample Species
649989998 Shigella dysenteriae
637000261 Shigella boydii
637000265 Shigella flexneri
640427143 Shigella sonnei
645058835 Shigella sp.In contrast, without sampling:
$ img_metadata_scanner.rb --output-fields "taxon_oid,Genus,Species" Genus=Shigella
649989998 Shigella dysenteriae
641522650 Shigella boydii
637000263 Shigella flexneri
637000265 Shigella flexneri
638341196 Shigella dysenteriae
637000264 Shigella flexneri
637000261 Shigella boydii
640427143 Shigella sonnei
646862341 Shigella flexneri
640427142 Shigella dysenteriae
645058835 Shigella sp.The metadata file
The data comes from a metadata file, which is obtained through the instructions available from the bio-img_metadata biogem documentation. You can specify the location of
this file to the script using the --img-metadata-file flag, or you can set the IMG_METADATA_FILE environment
variable if you are too lazy to type it in each time.
Copyright
Copyright (c) 2013 Ben J. Woodcroft. See LICENSE.txt for further details.