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

Make xrefs between Ensembl IDs and Uniprot IDs in STRING ingest #237

Merged
merged 10 commits into from
Jun 18, 2020
Merged

Make xrefs between Ensembl IDs and Uniprot IDs in STRING ingest #237

merged 10 commits into from
Jun 18, 2020

Commits on Jun 16, 2020

  1. Added item in STRING section of download.yaml for HUMAN_9606_idmappin… 

    …g.dat.gz
    @justaddcoffee
    justaddcoffee committed Jun 16, 2020
    Configuration menu
    Copy the full SHA
    b287df5 View commit details
    Browse the repository at this point in the history

Commits on Jun 17, 2020

  1. Some tests for STRING

    @justaddcoffee
    justaddcoffee committed Jun 17, 2020
    Configuration menu
    Copy the full SHA
    651a37e View commit details
    Browse the repository at this point in the history

  2. Fixed test, simplified code to add nodes/edges for xref to Uniprot IDs

    @justaddcoffee
    justaddcoffee committed Jun 17, 2020
    Configuration menu
    Copy the full SHA
    88cf6ad View commit details
    Browse the repository at this point in the history

  3. Moved code to write/edges for xref to Uniprot IDs

    @justaddcoffee
    justaddcoffee committed Jun 17, 2020
    Configuration menu
    Copy the full SHA
    134a62e View commit details
    Browse the repository at this point in the history

  4. Moved code to write/edges for xref to Uniprot IDs

    @justaddcoffee
    justaddcoffee committed Jun 17, 2020
    Configuration menu
    Copy the full SHA
    4afc529 View commit details
    Browse the repository at this point in the history

  5. Moved code to write protein nodes out of block that write gene -> pro… 

    …tein edges - I think that's a bug
    @justaddcoffee
    justaddcoffee committed Jun 17, 2020
    Configuration menu
    Copy the full SHA
    44e7df1 View commit details
    Browse the repository at this point in the history

  6. Better tests for nodes and edges tsv files in STRING

    @justaddcoffee
    justaddcoffee committed Jun 17, 2020
    Configuration menu
    Copy the full SHA
    d7f3d9d View commit details
    Browse the repository at this point in the history

  7. Added some ids to test ids make sure we're getting Ensembl to Uniprot… 

    … mapping stuff
    @justaddcoffee
    justaddcoffee committed Jun 17, 2020
    Configuration menu
    Copy the full SHA
    d6a052f View commit details
    Browse the repository at this point in the history

  8. Test failing for trivial reason

    @justaddcoffee
    justaddcoffee committed Jun 17, 2020
    Configuration menu
    Copy the full SHA
    e388719 View commit details
    Browse the repository at this point in the history

  9. Refactor such that Uniprot IDs are node properties in xrefs column (i… 

    …nstead of edges)
    @justaddcoffee
    justaddcoffee committed Jun 17, 2020
    Configuration menu
    Copy the full SHA
    cf1672d View commit details
    Browse the repository at this point in the history