Added transcripts and coordinates as accepted inputs in the TSV file.

[RSWilson1]

PR changes:

• Added transcripts and coordinates as accepted inputs
• Added initial draft for constructing VCF for testing bed annotation with VEP.
• Made some formatting and clarity changes
• Moved creation of bed file into it's own function.
• Created function to convert coordinates from TSV into bed format.
• Added unit tests

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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 construct_vcf.py:

Line 3:80: E501 line too long (80 > 79 characters) Line 67:80: E501 line too long (83 > 79 characters) Line 77:80: E501 line too long (84 > 79 characters) Line 82:80: E501 line too long (83 > 79 characters) Line 107:18: E124 closing bracket does not match visual indentation

• In the file gene_annotation2bed.py:

Line 68:80: E501 line too long (81 > 79 characters) Line 157:80: E501 line too long (82 > 79 characters) Line 158:80: E501 line too long (85 > 79 characters) Line 159:80: E501 line too long (86 > 79 characters) Line 160:80: E501 line too long (82 > 79 characters) Line 161:80: E501 line too long (83 > 79 characters) Line 162:80: E501 line too long (83 > 79 characters) Line 165:80: E501 line too long (84 > 79 characters) Line 166:80: E501 line too long (82 > 79 characters) Line 169:80: E501 line too long (83 > 79 characters) Line 174:80: E501 line too long (80 > 79 characters) Line 247:80: E501 line too long (80 > 79 characters) Line 256:80: E501 line too long (83 > 79 characters) Line 271:80: E501 line too long (81 > 79 characters) Line 272:80: E501 line too long (82 > 79 characters) Line 346:80: E501 line too long (90 > 79 characters) Line 366:80: E501 line too long (80 > 79 characters)

• In the file igv_report.py:

Line 50:80: E501 line too long (81 > 79 characters)

• In the file tests/test_gene_2annotation_script.py:

Line 18:1: E402 module level import not at top of file

• In the file tests/test_gff_parsing.py:

Line 7:1: E402 module level import not at top of file Line 162:80: E501 line too long (85 > 79 characters) Line 177:80: E501 line too long (87 > 79 characters) Line 192:80: E501 line too long (80 > 79 characters) Line 193:80: E501 line too long (82 > 79 characters) Line 198:80: E501 line too long (85 > 79 characters)

Comment last updated at 2023-10-17 13:39:49 UTC