Importing PFAM Images

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Wormbase genes are assigned PFAM domains and these domains are displayed on the gene page. For some of the PFAM domains, PFAM site contains protein structure images for proteins that contain the domain. A sample image is retrieved when available and displayed in a baloon tip for these domains on the Wormbase gene page.

To update the images:

Code: $WORMBASE/util/import_export/compile_pfam_images/
  • Make a list of PFAM domains in Wormbase: > pfam_ids.txt
  • Make a list of URLS using the script. This script expects a directory and stores all information in the specified directory. A file named pfam_index.log is created.
  • Acquire the images by running with the pfam_index.log file. You can specify the same directory to this script. Acquired images are stored in the directory.
  • Create thumbnails of the images acquired.
Thumbnail script: $WORMBASE/util/import_export// 
  • Move the thumbnail directory to:

  • Symlink to this directory from: