rip perl spaghetti

[jethror1]

Structure

• generate_workbook.py :
  • mostly just argparse related things
  • main() calls functions to process vcfs (reading, filtering, formatting etc.) then writing to file
• columns.py:
  • functions for splitting INFO and FORMAT/SAMPLE fields to separate columns
• filters.py:
  • functions for handling running bcftools filter and modifying incorrect field types in VCF header
• vcf.py:
  • main functions for doing all the vcf munging, process() contains the main logic for this
• excel.py:
  • functions for writing to and formatting output Excel file

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This change is 

[pep8speaks]

Hello @jethror1! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file resources/home/dnanexus/generate_workbook/generate_workbook.py:

Line 31:5: E303 too many blank lines (2) Line 45:5: E303 too many blank lines (2) Line 200:5: E303 too many blank lines (2) Line 217:5: E303 too many blank lines (2) Line 231:5: E303 too many blank lines (2) Line 262:5: E303 too many blank lines (2)

• In the file resources/home/dnanexus/generate_workbook/tests/test_columns.py:

Line 13:1: E402 module level import not at top of file Line 14:1: E402 module level import not at top of file Line 15:1: E402 module level import not at top of file Line 83:5: E303 too many blank lines (2) Line 92:31: W605 invalid escape sequence '_' Line 92:33: W605 invalid escape sequence '-' Line 92:35: W605 invalid escape sequence '.' Line 105:5: E303 too many blank lines (2) Line 114:34: W605 invalid escape sequence '.' Line 114:37: W605 invalid escape sequence '-' Line 125:80: E501 line too long (80 > 79 characters) Line 137:80: E501 line too long (83 > 79 characters) Line 145:5: E303 too many blank lines (2) Line 172:5: E303 too many blank lines (2)

• In the file resources/home/dnanexus/generate_workbook/tests/test_filters.py:

Line 15:1: E402 module level import not at top of file Line 16:1: E402 module level import not at top of file Line 17:1: E402 module level import not at top of file Line 18:1: E402 module level import not at top of file Line 61:5: E303 too many blank lines (2) Line 77:5: E303 too many blank lines (2) Line 82:80: E501 line too long (81 > 79 characters) Line 116:1: E303 too many blank lines (3) Line 144:5: E303 too many blank lines (2) Line 144:80: E501 line too long (83 > 79 characters) Line 189:5: E303 too many blank lines (2) Line 209:5: E303 too many blank lines (2) Line 230:5: E303 too many blank lines (2) Line 243:80: E501 line too long (81 > 79 characters) Line 246:9: E303 too many blank lines (2) Line 264:5: E303 too many blank lines (2)

• In the file resources/home/dnanexus/generate_workbook/tests/test_vcf.py:

Line 14:1: E402 module level import not at top of file Line 15:1: E402 module level import not at top of file Line 16:1: E402 module level import not at top of file Line 35:5: E303 too many blank lines (2) Line 50:5: E303 too many blank lines (2) Line 60:5: E303 too many blank lines (2) Line 113:5: E303 too many blank lines (2) Line 135:5: E303 too many blank lines (2) Line 154:5: E303 too many blank lines (2) Line 174:5: E303 too many blank lines (2) Line 230:5: E303 too many blank lines (2) Line 245:5: E303 too many blank lines (2)

• In the file resources/home/dnanexus/generate_workbook/utils/columns.py:

Line 36:5: E303 too many blank lines (2) Line 57:5: E303 too many blank lines (2) Line 128:5: E303 too many blank lines (2) Line 172:80: E501 line too long (83 > 79 characters) Line 201:9: E303 too many blank lines (2)

• In the file resources/home/dnanexus/generate_workbook/utils/excel.py:

Line 55:5: E303 too many blank lines (2) Line 66:5: E303 too many blank lines (2) Line 77:5: E303 too many blank lines (2) Line 135:80: E501 line too long (80 > 79 characters) Line 178:38: E231 missing whitespace after ',' Line 219:5: E303 too many blank lines (2) Line 268:5: E303 too many blank lines (2) Line 316:5: E303 too many blank lines (2) Line 332:5: E303 too many blank lines (2) Line 347:5: E303 too many blank lines (2) Line 404:5: E303 too many blank lines (2)

• In the file resources/home/dnanexus/generate_workbook/utils/filters.py:

Line 31:5: E303 too many blank lines (2) Line 75:5: E303 too many blank lines (2) Line 124:5: E303 too many blank lines (2) Line 167:5: E303 too many blank lines (2)

• In the file resources/home/dnanexus/generate_workbook/utils/vcf.py:

Line 52:80: E501 line too long (90 > 79 characters) Line 53:80: E501 line too long (83 > 79 characters) Line 57:5: E303 too many blank lines (2) Line 131:9: E303 too many blank lines (2) Line 158:5: E303 too many blank lines (2) Line 198:5: E303 too many blank lines (2) Line 226:5: E303 too many blank lines (2) Line 271:5: E303 too many blank lines (2) Line 322:5: E303 too many blank lines (2) Line 340:80: E501 line too long (81 > 79 characters) Line 346:5: E303 too many blank lines (2) Line 352:80: E501 line too long (87 > 79 characters) Line 376:5: E303 too many blank lines (2) Line 395:13: E125 continuation line with same indent as next logical line Line 396:17: E117 over-indented (comment) Line 397:17: E117 over-indented Line 414:5: E303 too many blank lines (2) Line 434:5: E303 too many blank lines (2) Line 448:5: E303 too many blank lines (2) Line 462:5: E303 too many blank lines (2) Line 502:5: E303 too many blank lines (2) Line 530:5: E303 too many blank lines (2) Line 562:56: W605 invalid escape sequence '\ ' Line 577:5: E303 too many blank lines (2) Line 587:80: E501 line too long (85 > 79 characters) Line 592:5: E303 too many blank lines (2)

Comment last updated at 2022-03-18 14:37:20 UTC