Refactor branch

[RSWilson1]

PR for refactoring

• Re-organised scripts into subfolders scripts and utils.
• Split-out a large function in gene_annotation2bed.py
• Updated tests to reflect changes
• Added some tests for functions in gene_annotation2bed.py
  • write_bed function
  • merge_overlapping function
  • subtract_and_replace function

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This change is 

[pep8speaks]

Hello @RSWilson1! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file gene_annotation2bed.py:

Line 167:80: E501 line too long (81 > 79 characters) Line 168:80: E501 line too long (82 > 79 characters) Line 174:80: E501 line too long (80 > 79 characters) Line 341:80: E501 line too long (92 > 79 characters) Line 342:80: E501 line too long (95 > 79 characters) Line 360:80: E501 line too long (88 > 79 characters)

• In the file tests/test_gene_annotation2bed.py:

Line 28:1: E302 expected 2 blank lines, found 1 Line 123:80: E501 line too long (80 > 79 characters) Line 124:80: E501 line too long (81 > 79 characters) Line 288:80: E501 line too long (81 > 79 characters) Line 375:80: E501 line too long (84 > 79 characters) Line 401:80: E501 line too long (83 > 79 characters) Line 453:80: E501 line too long (94 > 79 characters) Line 500:80: E501 line too long (88 > 79 characters) Line 504:80: E501 line too long (87 > 79 characters)

• In the file tests/test_gff_parsing.py:

Line 7:1: E402 module level import not at top of file

Comment last updated at 2024-02-02 10:39:32 UTC