Difference between revisions of "UniProtKB gpad to WormBase .ace"
From WormBaseWiki
Jump to navigationJump to search| Line 10: | Line 10: | ||
**gp2protein.wb file that maps UniProtKB IDs to WBGenes | **gp2protein.wb file that maps UniProtKB IDs to WBGenes | ||
**go_gpad_parser.pl | **go_gpad_parser.pl | ||
| + | |||
| + | *The go_gpad_parse.pl generates three files: | ||
| + | **gpad_extra_column - a file that adds the WBGene ID as an extra column (a new column 2) to the gpad file | ||
| + | **gpad_extra_column.err - a file that indicates which UniProtKB IDs don't map to WBGene IDs in the gp2protein.wb file | ||
| + | **gp_annotation.ace - the .ace file for upload to citace | ||
Revision as of 19:24, 24 February 2015
- The gpad file that contains all of the C. elegans annotations currently in Protein2GO is produced by UniProtKB on a weekly basis.
- A new file is available every Monday.
- The file is located here: ftp://ftp.ebi.ac.uk/pub/contrib/goa/ and is named: gp_association.6239_wormbase.gz
- Download the file from the UniProtKB ftp link and put it on tazendra here (in the appropriate year and month directory):
- /home/acedb/kimberly/citace_upload/go/gpad2ace
- for example: /home/acedb/kimberly/citace_upload/go/gpad2ace/2015_February
- To convert the gpad file to a .ace file you'll need:
- gp2protein.wb file that maps UniProtKB IDs to WBGenes
- go_gpad_parser.pl
- The go_gpad_parse.pl generates three files:
- gpad_extra_column - a file that adds the WBGene ID as an extra column (a new column 2) to the gpad file
- gpad_extra_column.err - a file that indicates which UniProtKB IDs don't map to WBGene IDs in the gp2protein.wb file
- gp_annotation.ace - the .ace file for upload to citace
