Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

ADD missing ARO mappings to manual curation #48

Merged
merged 7 commits into from
Jun 9, 2024
Merged

ADD missing ARO mappings to manual curation #48

merged 7 commits into from
Jun 9, 2024

Conversation

Vedanth-Ramji
Copy link
Member

@Vedanth-Ramji Vedanth-Ramji commented Jun 1, 2024 •
edited
Loading

Additions:

  • argannot_curation: (Phe)cpt_strepv:U09991:AAB36569:1412-1948:537 -> ARO: 3000249
  • megares_curation: MEG_2114 -> ARO: 3000249, MEG_2430 -> ARO: 3000016, MEG_985 -> ARO: 3000229, MEG_2865 -> ARO:3000387, MEG_7974 -> ARO:3000076
  • sarg_curation: AM180355.1.gene2260.p01 -> ARO: 3000250
  • resfinder_curation: dldHA2X_1_AL939117 -> ARO:3003970, grdA_1_QJX10702 -> ARO:3007382, EstDL136_1_JN242251 -> ARO:3000387
  • resfinderfg_curation: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase|KF629588.1|pediatric_fecal_sample|CYC -> ARO:3003970
  • deeparg_curation: gi:447201629:ref:WP_001278885.1:|FEATURES|cob(I)alamin_adenolsyltransferase|unclassified|cob(I)alamin_adenolsyltransferase -> ARO:0010004

luispedro
luispedro reviewed Jun 1, 2024
View reviewed changes
luispedro
luispedro requested changes Jun 1, 2024
View reviewed changes
Copy link
Member

@luispedro luispedro left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Besides the comment about the tests, can you also add this to the changelog?

@luispedro
Copy link
Member

Right now, the resfinder table has a column for Description, but none of the other ones do. Ideally, this would be more common, but maybe we can start adding descriptions for the new entries going forward?

@Vedanth-Ramji Vedanth-Ramji marked this pull request as ready for review June 4, 2024 17:11
@Vedanth-Ramji
Copy link
Member Author

I have gone ahead and added the descriptions for the updated manual curation files

@luispedro
Copy link
Member

Looks good. Can you rebase on the current main?

@Vedanth-Ramji
ADD missing ARO mappings to manual curation
830c86d 
A few ARO mappings were missing in the manual curation and they have been added. A few more missing manual curation genes from NCBI, MEGARes, and DeepARG will be added.

Additions:
- argannot_curation: (Phe)cpt_strepv:U09991:AAB36569:1412-1948:537 -> ARO: 3000249
- megares_curation: MEG_2114 -> ARO: 3000249, MEG_2430 -> ARO: 3000016, MEG_985 -> ARO: 3000229
- sarg_curation: AM180355.1.gene2260.p01 -> ARO: 3000250

Update test_lib expected output for updated manual curation

Add test case where map_to_aro() returns None

This had to be done as (Phe)cpt_strepv:U09991:AAB36569:1412-1948:537 was given an ARO mapping in the manual curation which previously was not present
@Vedanth-Ramji
ADD rest of missing manual curations in megares manual curation
b7c7f26 
Additions:
MEG_2865 -> ARO:3000387
MEG_7974 -> ARO:3000076
@Vedanth-Ramji
Added missing manual curations for resfinder & resfinderfg
afcf717 
Additions:
resfinder_curation: dldHA2X_1_AL939117 -> ARO:3003970, grdA_1_QJX10702 -> ARO:3007382, EstDL136_1_JN242251 -> ARO:3000387
resfinderfg_curation: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase|KF629588.1|pediatric_fecal_sample|CYC -> ARO:3003970
@Vedanth-Ramji
Update outputs for addition of missing manual curations for resfinder…
fa946df 
… & resfinderfg
@Vedanth-Ramji
DOC add descriptions for new manual curation files
135ae28
@Vedanth-Ramji Vedanth-Ramji force-pushed the update_manual_curation branch from d2b380d to 135ae28 Compare June 7, 2024 15:03
@Vedanth-Ramji
Copy link
Member Author

I have gone ahead and rebased the commits. It should be ready to merge now

luispedro
luispedro requested changes Jun 8, 2024
View reviewed changes
@luispedro luispedro merged commit 7da7beb into BigDataBiology:main Jun 9, 2024
6 checks passed
@Vedanth-Ramji Vedanth-Ramji deleted the update_manual_curation branch June 9, 2024 18:16
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@luispedro luispedro luispedro approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@Vedanth-Ramji @luispedro