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Development Branch #46

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merged 47 commits into from
Oct 10, 2017
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b872e36
Removed Stuart's experimental analysis scripts. These are ready to us…
biomadeira Oct 3, 2017
7549ade
Refactoring: moved the tests data to 'testdata' folder and renamed th…
biomadeira Oct 3, 2017
f3547d7
Refactoring: renamed the tests and joined the two 'uniprot' test cases.
biomadeira Oct 3, 2017
73d3955
Improved the `get_url_or_retry` (now `fetch_from_url_or_retry`) funct…
biomadeira Oct 3, 2017
8618074
Improved the `_table_selector` method (now `row_selector`) function. …
biomadeira Oct 3, 2017
3f66a9b
Refactoring: Moved DSSP and SIFTS functions to their own file. Also u…
biomadeira Oct 3, 2017
68d0237
Added generic classes to validate input/output file paths. Also added…
biomadeira Oct 3, 2017
4fb599b
Added two new generic functions for coercing data types and to remove…
biomadeira Oct 3, 2017
b682868
Improved the `_mmcif_atom` (now `parse_mmcif_atoms`) for using the ge…
biomadeira Oct 3, 2017
4343359
Added a new generic method for parsing PDB atom lines onto a mmCIF-li…
biomadeira Oct 4, 2017
e51511c
Improved the `_dssp` (now `parse_dssp_residues`) for using the generi…
biomadeira Oct 4, 2017
1e81c17
Improved the `_sifts_residues_regions` (now `parse_sifts_residues`) f…
biomadeira Oct 4, 2017
7809e50
Added a new generic Downloader class that generalises downloading and…
biomadeira Oct 4, 2017
1a35600
Added new functions to write in mmCIF and PDB format from both the PD…
biomadeira Oct 4, 2017
62d10d4
Improved the `_residues_as_centroid` (now `residues_aggregation`) to…
biomadeira Oct 4, 2017
75c682b
Added a new (super) class for generalising typical inputs and getter/…
biomadeira Oct 4, 2017
ff3800c
Improved the `select_cif` (now `select_structures`) to use a new `fil…
biomadeira Oct 5, 2017
2b0d5e7
Added some new wrapper methods/classes for accessing the various read…
biomadeira Oct 5, 2017
b824805
Refactoring: Removed unnecessary 'config.txt' found on the tests dir.
biomadeira Oct 5, 2017
dd426ca
Improved the `select_dssp` to use a new `filter_dssp` function that a…
biomadeira Oct 5, 2017
6e60548
Added some new wrapper methods/classes for accessing the various read…
biomadeira Oct 5, 2017
9b38438
Improved the `select_sifts` to use a new `filter_sifts` function that…
biomadeira Oct 5, 2017
7e937fe
Added some new wrapper methods/classes for accessing the various read…
biomadeira Oct 5, 2017
65cd0c5
Refactoring: removed unnecessary SIFTS gz files.
biomadeira Oct 5, 2017
58e2d5f
Minor updates to include the config.txt and excluded 'requests_cache'…
biomadeira Oct 5, 2017
4ea612c
Moved the validation functions to a new validation.py. Improved the `…
biomadeira Oct 6, 2017
362b839
Refactoring: fixed the paths to files and improved the consistency of…
biomadeira Oct 6, 2017
c1e8a2b
Refactoring: removed the python shebang and improved pep8 for more i…
biomadeira Oct 6, 2017
9c4ec1d
Refactoring: improved logging loading across the board for consistency.
biomadeira Oct 6, 2017
7ec1c56
Added some new wrapper methods/classes for accessing the various read…
biomadeira Oct 6, 2017
fd89c22
Refactoring: moved 'uniprot.py' to annotation and the variant-related…
biomadeira Oct 6, 2017
bcd5f39
Several improvements of the 'annotation.py' methods. Added some new w…
biomadeira Oct 6, 2017
3d03f7f
Refactoring: Moved some variants-related functions from the utils and…
biomadeira Oct 6, 2017
96935ed
Refactoring: removed unnecessary and untested functions. Also some mi…
biomadeira Oct 6, 2017
1918dbf
Refactoring: moved from config.txt to config.ini (better pycharm supp…
biomadeira Oct 6, 2017
4b9ca18
Added new utilities for flattening very nested json structures. These…
biomadeira Oct 8, 2017
9054664
Moved the tests from 'test_ensembl' to 'test_variants'. Made some cha…
biomadeira Oct 8, 2017
7f4781c
Added some new wrapper methods/classes for accessing the various fetc…
biomadeira Oct 9, 2017
4a0bcdc
Refactoring: moved the `get_preferred_assembly_id` and `fetch_summary…
biomadeira Oct 9, 2017
286e658
Refactoring: improved the `sifts_best` for using another existing met…
biomadeira Oct 9, 2017
9ce2609
Refactoring: moved the `merge_tables` function to 'mergers.py'. This …
biomadeira Oct 9, 2017
01e67b7
Added new 'merger' functions and some new wrapper methods/classes for…
biomadeira Oct 9, 2017
c471a30
Added a new option to `filter_validation` to add 'validation_resnum_f…
biomadeira Oct 10, 2017
da4615f
Added new merging methods for Validation, Annotation and Variants. Al…
biomadeira Oct 10, 2017
07dc7da
Various fixes to make Table Merging more consistent. Also added a new…
biomadeira Oct 10, 2017
9d268b0
Moved to use the new `Tables.generator()` for the main CLI and in the…
biomadeira Oct 10, 2017
daba468
Setup.py `install_requirements` are read from requirements.txt. Also …
biomadeira Oct 10, 2017
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2 changes: 1 addition & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@ env
._*
.DS_Store
__pycache__
config.txt
.ipynb_checkpoints
.tox/
*.egg-info
Expand All @@ -14,3 +13,4 @@ docs/_static/
docs/_templates/
notebooks/
proteofav/analysis/
tests/*.sqlite
14 changes: 10 additions & 4 deletions __main__.py
Original file line number Diff line number Diff line change
@@ -1,12 +1,18 @@
#!/usr/bin/env python
# -*- coding: utf-8

"""
Created on 14:18 17/02/2017 2017
ProteoFAV: Protein Feature Aggregation and Variants
---------------------------------------------------

Open-source framework for simple and fast integration
of protein structure data with sequence annotations
and genetic variation

:copyright: (c) 2015-2017.
:license: TBD, see LICENSE for more details.
"""
from __future__ import absolute_import

from proteofav.main import main

if __name__ == '__main__':
main()
main()
Empty file removed analysis/__init__.py
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