For #887 #669
Merged
For #887 #669
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
@dustine32 thanks for reviewing quickly. |
mugitty
deleted the
go-site-887-gorule-0000005-some-codes-are-not-allowed-for-protein-binding-or-binding
branch
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Testing with the following GAF lines:
! TBC FAILS GORULE:0000005 - TEST 1 - incorrect evidence codes for 'protein binding ; GO:0005515' - ISS not allowed
UniProtKB O76187 darA enables GO:0005515 PMID:9802899 ISS UniProtKB:P34149 F GORULE_TEST:0000005-1 Darlin darA protein taxon:44689 20100205 GO_Central
! TBC FAILS GORULE:0000005 - TEST 2 - incorrect evidence codes for 'protein binding ; GO:0005515' - IS0 not allowed
UniProtKB O76187 darA enables GO:0005515 PMID:9802899 ISO UniProtKB:P34149 F GORULE_TEST:0000005-2 Darlin darA protein taxon:44689 20100205 GO_Central
! TBC FAILS GORULE:0000005 - TEST 3 - incorrect evidence codes for 'protein binding ; GO:0005515' - IBA not allowed
UniProtKB O76187 darA enables GO:0005515 GO_REF:0000033 IBA UniProtKB:P34149 F GORULE_TEST:0000005-3 Darlin darA protein taxon:44689 20100205 GO_Central
Resulted in the following errors:
"gorule-0000005": [
{
"level": "WARNING",
"line": "UniProtKB\tO76187\tdarA\tenables\tGO:0005515\tPMID:9802899\tISS\tUniProtKB:P34149\tF\tGORULE_TEST:0000005-1 Darlin\tdarA\tprotein\ttaxon:44689\t20100205\tGO_Central\t\n",
"type": "Violates GO Rule",
"message": "GORULE:0000005: IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae not allowed for direct annotations to 'binding ; GO:0005488' or 'protein binding ; GO:0005515'",
"obj": "",
"taxon": "",
"rule": 5
},
{
"level": "WARNING",
"line": "UniProtKB\tO76187\tdarA\tenables\tGO:0005515\tPMID:9802899\tISO\tUniProtKB:P34149\tF\tGORULE_TEST:0000005-2 Darlin\tdarA\tprotein\ttaxon:44689\t20100205\tGO_Central\t\n",
"type": "Violates GO Rule",
"message": "GORULE:0000005: IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae not allowed for direct annotations to 'binding ; GO:0005488' or 'protein binding ; GO:0005515'",
"obj": "",
"taxon": "",
"rule": 5
},
{
"level": "WARNING",
"line": "UniProtKB\tO76187\tdarA\tenables\tGO:0005515\tGO_REF:0000033\tIBA\tUniProtKB:P34149\tF\tGORULE_TEST:0000005-3 Darlin\tdarA\tprotein\ttaxon:44689\t20100205\tGO_Central\t\n",
"type": "Violates GO Rule",
"message": "GORULE:0000005: IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae not allowed for direct annotations to 'binding ; GO:0005488' or 'protein binding ; GO:0005515'",
"obj": "",
"taxon": "",
"rule": 5
}
],
Also, unrelated IBA for PAINT error
"gorule-0000026": [
{
"level": "ERROR",
"line": "UniProtKB\tO76187\tdarA\tenables\tGO:0005515\tGO_REF:0000033\tIBA\tUniProtKB:P34149\tF\tGORULE_TEST:0000005-3 Darlin\tdarA\tprotein\ttaxon:44689\t20100205\tGO_Central\t\n",
"type": "Violates GO Rule",
"message": "GORULE:0000026: IBA evidence codes should be filtered from main MOD gaf sources",
"obj": "",
"taxon": "",
"rule": 26
},