A collection of scripts dealing with local stores of IMG data.


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
Methanobacterium    sp.
Sulfolobus  islandicus
Desulfurococcus mucosus
Haladaptatus    paucihalophilus
Methanothermobacter thermautotrophicus
Methanosarcina  barkeri
Methanobrevibacter  smithii

Print out the headers available for filtering or reporting

$ img_metadata_scanner.rb -l |less
Proposal Name

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 below. 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.

Go to IMG > Genome Browser:

In the Table Configuration section:

  • Genome Field > Click All
  • Project Metadata > Click All
  • Data Statistics > Click All

Click Display Genomes Again. In the Genome Browser section > Click Select All. Finally, click the Export button.

PS/ Don't trust the IMG metadata too much. There are some big mistakes, e.g. in the 16S copy number

PS2/ What have I done to create the FIXED metadata?

  • I have deleted two occurences of "\r" (^M) by ""
  • taxonoid 2515154013 has two extra fields: remove the two cells containing "Human wound, cranian"
  • Replace cells containing "-1" by ""
  • Replaced 'Marine archaeal group 1 BG20 (Nitrosoarchaeum limnia BG20)' by 'Nitrosoarchaeum limnia BG20'

(Download instructions kindly contributed by @fangly / Florent Angly)

Copyright (c) 2013 Ben J. Woodcroft. See LICENSE.txt for further details.