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Xref parser zfin

Marek Szuba requested to merge xref_parser_zfin into feature/xref_sprint

Created by: ens-bwalts

Requirements

  • Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
  • Review the contributing guidelines for this repository; remember in particular:
    • do not modify code without testing for regression
    • provide simple unit tests to test the changes
    • if you change the schema you must patch the test databases as well, see Updating the schema
    • the PR must not fail unit testing

Description

Change parser to utilize Text::CSV. Change parser to use ZFIN files that now contain four columns. Rename functions for clarity

Restrict Uniprot source to only use SwissProt

Use case

Parser is updated to meet new xref standards (Text::CSV). Cleanup for readability. Should now work with ZFIN source files

Benefits

See under Use Case

Possible Drawbacks

Adds dependency to Text::CSV.

Testing

Parser works and adds xrefs in the context of the xref pipeline as it stands in early November.

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