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Development Branch#46

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biomadeira merged 47 commits intomasterbartongroup/ProteoFAV:masterfrom developmentbartongroup/ProteoFAV:developmentCopy head branch name to clipboardOct 10, 2017

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Commits

Commits on Oct 3, 2017

• Removed Stuart's experimental analysis scripts. These are ready to use in a branch called experimental_analysis_branch.

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• Refactoring: moved the tests data to 'testdata' folder and renamed the folders. Also updated the references to the data in the tests.

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• Refactoring: renamed the tests and joined the two 'uniprot' test cases.

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Commits on Oct 4, 2017

• Improved the get_url_or_retry (now fetch_from_url_or_retry) function. Also added new tests for the fetcher and updated references/tests.

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• Improved the _table_selector method (now row_selector) function. Also added new tests for the function and updated references/tests.

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• Refactoring: Moved DSSP and SIFTS functions to their own file. Also updated the references/tests.

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• Added generic classes to validate input/output file paths. Also added some basic tests.

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Commits on Oct 6, 2017

• Added two new generic functions for coercing data types and to remove excluded columns. This fails to coerce the columns if there are nans in the column. Also added corresponding tests.

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• Improved the _mmcif_atom (now parse_mmcif_atoms) for using the generic methods for constraining types and removing unecessary columns. Also updated references/tests and added new tests.

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• Added a new generic method for parsing PDB atom lines onto a mmCIF-like pandas DataFrame (same table headers) . Also added corresponding tests.

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• Improved the _dssp (now parse_dssp_residues) for using the generic methods for constraining types and removing unecessary columns. Also updated references/tests and added new tests.

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• Improved the _sifts_residues_regions (now parse_sifts_residues) for using the generic methods for constraining types and removing unecessary columns. Also updated references/tests and added new…

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• Added a new generic Downloader class that generalises downloading and uncompressing of files from urls. Also added some minimal tests.

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• Added new functions to write in mmCIF and PDB format from both the PDB/mmCIF parsed DataFrames. Also added corresponding tests.

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• Improved the _residues_as_centroid (now residues_aggregation) to make it more generic and complete. Also updated references/tests and added new tests.

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• Added a new (super) class for generalising typical inputs and getter/setter methods used to interface a main class (e.g. PDB, mmCIF, DSSP, etc. - to be implemented). Also added corresponding tests.

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• Improved the select_cif (now select_structures) to use a new filter_structures function that allows for additional filtering. Also updated references/tests and added new tests for the additio…

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• Added some new wrapper methods/classes for accessing the various reading/writting/downloading/selecting mmCIFs and PDBs. Also added corresponding tests.

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• Refactoring: Removed unnecessary 'config.txt' found on the tests dir.

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• Improved the select_dssp to use a new filter_dssp function that allows for additional filtering. Also updated references/tests and added new tests for the additional functions get_rsa and `ge…

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• Added some new wrapper methods/classes for accessing the various reading/downloading/selecting DSSPs. Also added corresponding tests.

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• Improved the select_sifts to use a new filter_sifts function that allows for additional filtering. Also updated references/tests and added new tests.

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• Added some new wrapper methods/classes for accessing the various reading/downloading/selecting SIFTS. Also added corresponding tests.

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• Refactoring: removed unnecessary SIFTS gz files.

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• Minor updates to include the config.txt and excluded 'requests_cache' dbs.

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• Moved the validation functions to a new validation.py. Improved the _pdb_validation_to_table (now parse_validation_residues) using the generic methods for constraining types. Also updated refer…

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• Refactoring: fixed the paths to files and improved the consistency of the use of os.path....

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• Refactoring: removed the python shebang and improved pep8 for more idiomatic python.

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• Refactoring: improved logging loading across the board for consistency.

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• Added some new wrapper methods/classes for accessing the various reading/downloading/selecting Validation Data. Also added corresponding tests and improved types consistency.

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• Refactoring: moved 'uniprot.py' to annotation and the variant-related functions to variants. Moved the tests accordingly.

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• Several improvements of the 'annotation.py' methods. Added some new wrapper methods/classes for accessing the various reading/downloading/selecting GFF annotations. Also improved the tests.

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• Refactoring: Moved some variants-related functions from the utils and moved the tests to 'test_variants.py'.

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• Refactoring: removed unnecessary and untested functions. Also some minor refactoring.

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• Refactoring: moved from config.txt to config.ini (better pycharm support) and improved some names for consistency

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Commits on Oct 8, 2017

• Added new utilities for flattening very nested json structures. These are alternatives to Pandas json_normalise and are going to be used to flatten Ensembl/UniProt Variants tables. Also added cor…

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Commits on Oct 9, 2017

• Moved the tests from 'test_ensembl' to 'test_variants'. Made some changes and added new functions. Also added some new tests.

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• Added some new wrapper methods/classes for accessing the various fetching/selecting Variation Data. Also added corresponding tests and improved types consistency.

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Commits on Oct 10, 2017

• Refactoring: moved the get_preferred_assembly_id and fetch_summary_properties_pdbe to the 'structures.py'. Removed unused functions. Also added new tests and made minor improvements for consist…

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• Refactoring: improved the sifts_best for using another existing method and increase consistency.

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• Refactoring: moved the merge_tables function to 'mergers.py'. This will used to implemented 'modular' merger functions and a Tables class.

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• Added new 'merger' functions and some new wrapper methods/classes for accessing the various data (via Table Generators and Merging). Also added new tests. More to come.

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• Added a new option to filter_validation to add 'validation_resnum_full' used for table merging. Also added corresponding test.

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• Added new merging methods for Validation, Annotation and Variants. Also added new tests.

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• Various fixes to make Table Merging more consistent. Also added a new tests.

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• Moved to use the new Tables.generator() for the main CLI and in the tests. More testing needed.

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• Setup.py install_requirements are read from requirements.txt. Also bumped the versions of the modules.

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