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Utils IO into ensembl-io

Marek Szuba requested to merge utils_io_move into master

Created by: tgrego

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  • 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

Using one or more sentences, describe in detail the proposed changes. Related to the the pull request https://github.com/Ensembl/ensembl-io/pull/79. IO code, and specially the reading/writing of bioinformatics file formats, should be contained in the same repo. Thus the code Bio::EnsEMBL::Utils::IO::* has been moved to the ensembl-io repo.

ensembl-io has been added to the travis builds, but it is not a requirement of the core ensembl repo. A single test requires it (fastaSequenceAdaptor.t) and is skipped if it's not present.

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. Most users of core will not notice this, those who use Bio::EnsEMBL::Utils::IO::* will need to add ensembl-io as a dependency.

Benefits

If applicable, describe the advantages the changes will have. Keep IO code in the same place, make core ensembl repo cleaner.

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes. Extra dependency for some users.

Testing

Have you added/modified unit tests to test the changes? yes

If so, do the tests pass/fail? yes

Have you run the entire test suite and no regression was detected? yes

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