Flake8 warnings

[zhx828]

Maybe worth to look into the warnings. These are generated through the github action.

./GenerateReadMe.py:4:1: F403 'from AnnotatorCore import *' used; unable to detect undefined names
./GenerateReadMe.py:14:9: F405 'sys' may be undefined, or defined from star imports: AnnotatorCore
./GenerateReadMe.py:18:9: F405 'sys' may be undefined, or defined from star imports: AnnotatorCore
./GenerateReadMe.py:20:9: F405 'setoncokbbaseurl' may be undefined, or defined from star imports: AnnotatorCore
./GenerateReadMe.py:22:5: F405 'generateReadme' may be undefined, or defined from star imports: AnnotatorCore
./StructuralVariantAnnotator.py:4:1: F403 'from AnnotatorCore import *' used; unable to detect undefined names
./StructuralVariantAnnotator.py:9:1: E302 expected 2 blank lines, found 1
./StructuralVariantAnnotator.py:12:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:12:128: E501 line too long (262 > 127 characters)
./StructuralVariantAnnotator.py:13:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:14:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:15:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:16:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:16:128: E501 line too long (184 > 127 characters)
./StructuralVariantAnnotator.py:17:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:18:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:19:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:20:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:21:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:22:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:23:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:24:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:25:9: E128 continuation line under-indented for visual indent
./StructuralVariantAnnotator.py:26:9: F405 'sys' may be undefined, or defined from star imports: AnnotatorCore
./StructuralVariantAnnotator.py:38:9: F405 'sys' may be undefined, or defined from star imports: AnnotatorCore
./StructuralVariantAnnotator.py:40:9: F405 'setsampleidsfileterfile' may be undefined, or defined from star imports: AnnotatorCore
./StructuralVariantAnnotator.py:42:9: F405 'setcancerhotspotsbaseurl' may be undefined, or defined from star imports: AnnotatorCore
./StructuralVariantAnnotator.py:44:9: F405 'setoncokbbaseurl' may be undefined, or defined from star imports: AnnotatorCore
./StructuralVariantAnnotator.py:45:5: F405 'setoncokbapitoken' may be undefined, or defined from star imports: AnnotatorCore
./StructuralVariantAnnotator.py:49:9: F405 'readCancerTypes' may be undefined, or defined from star imports: AnnotatorCore
./StructuralVariantAnnotator.py:51:5: F405 'validate_oncokb_token' may be undefined, or defined from star imports: AnnotatorCore
./StructuralVariantAnnotator.py:54:5: F405 'process_sv' may be undefined, or defined from star imports: AnnotatorCore
./FusionAnnotator.py:4:1: F403 'from AnnotatorCore import *' used; unable to detect undefined names
./FusionAnnotator.py:9:1: E302 expected 2 blank lines, found 1
./FusionAnnotator.py:12:9: E128 continuation line under-indented for visual indent
./FusionAnnotator.py:12:128: E501 line too long (299 > 127 characters)
./FusionAnnotator.py:12:279: W605 invalid escape sequence '\d'
./FusionAnnotator.py:12:291: W605 invalid escape sequence '\d'
./FusionAnnotator.py:13:9: E128 continuation line under-indented for visual indent
./FusionAnnotator.py:14:9: E128 continuation line under-indented for visual indent
./OncoKBPlots.py:22:9: E128 continuation line under-indented for visual indent
./OncoKBPlots.py:23:9: E128 continuation line under-indented for visual indent
./OncoKBPlots.py:24:9: F405 'sys' may be undefined, or defined from star imports: AnnotatorCore
./OncoKBPlots.py:34:9: F405 'sys' may be undefined, or defined from star imports: AnnotatorCore
./OncoKBPlots.py:36:9: F405 'setsampleidsfileterfile' may be undefined, or defined from star imports: AnnotatorCore
./OncoKBPlots.py:38:28: F405 're' may be undefined, or defined from star imports: AnnotatorCore
./OncoKBPlots.py:43:5: F405 'plotclinicalactionability' may be undefined, or defined from star imports: AnnotatorCore
./OncoKBPlots.py:48:5: F405 'plotclinicalactionability' may be undefined, or defined from star imports: AnnotatorCore
./OncoKBPlots.py:49:5: F405 'plotimplications' may be undefined, or defined from star imports: AnnotatorCore
./OncoKBPlots.py:49:81: F405 'dxLevels' may be undefined, or defined from star imports: AnnotatorCore
./OncoKBPlots.py:49:128: E501 line too long (132 > 127 characters)
./OncoKBPlots.py:50:5: F405 'plotimplications' may be undefined, or defined from star imports: AnnotatorCore
./OncoKBPlots.py:50:81: F405 'pxLevels' may be undefined, or defined from star imports: AnnotatorCore
./OncoKBPlots.py:50:128: E501 line too long (132 > 127 characters)
./OncoKBPlots.py:60:1: E305 expected 2 blank lines after class or function definition, found 1
./MafAnnotator.py:4:1: F403 'from AnnotatorCore import *' used; unable to detect undefined names
./MafAnnotator.py:[11](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:12):1: C901 'main' is too complex (16)
./MafAnnotator.py:16:[12](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:13)8: E501 line too long (164 > 127 characters)
./MafAnnotator.py:49:128: E501 line too long (145 > 127 characters)
./MafAnnotator.py:55:9: F405 'sys' may be undefined, or defined from star imports: AnnotatorCore
./MafAnnotator.py:67:9: F405 'sys' may be undefined, or defined from star imports: AnnotatorCore
./MafAnnotator.py:70:9: F405 'setsampleidsfileterfile' may be undefined, or defined from star imports: AnnotatorCore
./MafAnnotator.py:72:9: F405 'setcancerhotspotsbaseurl' may be undefined, or defined from star imports: AnnotatorCore
./MafAnnotator.py:74:9: F405 'setoncokbbaseurl' may be undefined, or defined from star imports: AnnotatorCore
./MafAnnotator.py:75:5: F405 'setoncokbapitoken' may be undefined, or defined from star imports: AnnotatorCore
./MafAnnotator.py:79:9: F405 'readCancerTypes' may be undefined, or defined from star imports: AnnotatorCore
./MafAnnotator.py:86:37: F405 'QueryType' may be undefined, or defined from star imports: AnnotatorCore
./MafAnnotator.py:89:128: E501 line too long ([13](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:14)5 > 127 characters)
./MafAnnotator.py:95:40: F405 'ReferenceGenome' may be undefined, or defined from star imports: AnnotatorCore
./MafAnnotator.py:101:5: F405 'validate_oncokb_token' may be undefined, or defined from star imports: AnnotatorCore
./MafAnnotator.py:103:5: F405 'processalterationevents' may be undefined, or defined from star imports: AnnotatorCore
./CnaAnnotator.py:4:1: F403 'from AnnotatorCore import *' used; unable to detect undefined names
./CnaAnnotator.py:13:9: E128 continuation line under-indented for visual indent
./CnaAnnotator.py:13:128: E501 line too long (281 > 127 characters)
./CnaAnnotator.py:[14](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:15):9: E128 continuation line under-indented for visual indent
./CnaAnnotator.py:14:128: E501 line too long (226 > 127 characters)
./CnaAnnotator.py:[15](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:16):9: E128 continuation line under-indented for visual indent
./CnaAnnotator.py:[16](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:17):9: E128 continuation line under-indented for visual indent
./CnaAnnotator.py:[17](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:18):9: E128 continuation line under-indented for visual indent
./CnaAnnotator.py:[18](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:19):9: E128 continuation line under-indented for visual indent
./CnaAnnotator.py:[19](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:20):9: E128 continuation line under-indented for visual indent
./CnaAnnotator.py:[20](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:21):9: E128 continuation line under-indented for visual indent
./CnaAnnotator.py:[21](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:22):9: E128 continuation line under-indented for visual indent
./CnaAnnotator.py:21:128: E501 line too long (169 > 127 characters)
./CnaAnnotator.py:[22](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:23):9: E128 continuation line under-indented for visual indent
./CnaAnnotator.py:[23](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:24):9: F405 'sys' may be undefined, or defined from star imports: AnnotatorCore
./CnaAnnotator.py:35:9: F405 'sys' may be undefined, or defined from star imports: AnnotatorCore
./CnaAnnotator.py:37:9: F405 'setsampleidsfileterfile' may be undefined, or defined from star imports: AnnotatorCore
./CnaAnnotator.py:39:9: F405 'setoncokbbaseurl' may be undefined, or defined from star imports: AnnotatorCore
./CnaAnnotator.py:40:5: F405 'setoncokbapitoken' may be undefined, or defined from star imports: AnnotatorCore
./CnaAnnotator.py:44:9: F405 'readCancerTypes' may be undefined, or defined from star imports: AnnotatorCore
./CnaAnnotator.py:46:5: F405 'validate_oncokb_token' may be undefined, or defined from star imports: AnnotatorCore
./CnaAnnotator.py:49:5: F405 'process_cna_data' may be undefined, or defined from star imports: AnnotatorCore
./CnaAnnotator.py:50:26: E127 continuation line over-indented for visual indent
./CnaAnnotator.py:67:63: F405 'CNA_FILE_FORMAT_GISTIC' may be undefined, or defined from star imports: AnnotatorCore
10    C901 'process_alteration' is too complex (16)
1     E127 continuation line over-indented for visual indent
53    E128 continuation line under-indented for visual indent
8     E2[25](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:26) missing whitespace around operator
11    E231 missing whitespace after ','
8     E[26](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:27)1 at least two spaces before inline comment
1     E262 inline comment should start with '# '
2     E301 expected 1 blank line, found 0
41    E302 expected 2 blank lines, found 1
7     E303 too many blank lines (2)
4     E305 expected 2 blank lines after class or function definition, found 1
4     E402 module level import not at top of file
35    E501 line too long (189 > 1[27](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:28) characters)
1     E712 comparison to False should be 'if cond is False:' or 'if not cond:'
4     E722 do not use bare 'except'
21    E741 ambiguous variable name 'l'
1     F401 'sys' imported but unused
9     F403 'from AnnotatorCore import *' used; unable to detect undefined names
254   F405 'sys' may be undefined, or defined from star imports: AnnotatorCore
8     F841 local variable 'posp' is assigned to but never used
7     W[29](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:30)3 blank line contains whitespace
5     W605 invalid escape sequence '\d'
[49](https://github.com/oncokb/oncokb-annotator/runs/6756316536?check_suite_focus=true#step:5:50)5