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Centralize "Split" File Path Generation #229

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Centralize "Split" File Path Generation #229

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tmooney
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@tmooney tmooney commented Nov 15, 2016

  • This PR should not affect the output of the pipelines. This was mostly an excuse to practice editing some Python code. 😄
  • I wasn't sure whether or not to replace the fasta_chunk variable used in each of the status messages. It might simplify the code a little by removing a variable.

susannasiebert
susannasiebert approved these changes Nov 15, 2016
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+1. I could go either way with replacing the fasta_chunk variable.

Glad to see a PR from someone that isn't me. There is certainly a lot of room for improvement in this code.

@tmooney tmooney force-pushed the centralize_split_file_path_generation branch from fc2dd34 to b4a7934 Compare November 21, 2016 15:45
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tmooney commented Nov 21, 2016

I've rebased this to resolve the conflicts with #200.

@tmooney tmooney force-pushed the centralize_split_file_path_generation branch from b4a7934 to 47a031d Compare December 1, 2016 22:47
@susannasiebert
Make generate_fasta into a class
2f37548
@susannasiebert
Make convert_vcf into a class
e43f463
@susannasiebert
Make parse_output into a class
dbba078
@susannasiebert
Change ParseOutput class name to OutputParser
9589f12
@susannasiebert
Change GenerateFasta class name to FastaGenerator
1619ed8
@susannasiebert
Change ConvertVcf class name to InputFileConverter
3cd44f4
@susannasiebert
Remove unneeded imports
e2b060b
@susannasiebert
Eliminate unnecessary conditionals
9184440
@susannasiebert
use with for opening filehandles where appropriate
5c9d23f
@susannasiebert
Update InputFileConverter to accept Integrate files
36f8a13
@susannasiebert
Update FastaGenerator to accept fusion tsv
d79cd10
@susannasiebert
Update OutputParser to be able to handle fusion output files
2e87ff4
@susannasiebert
Update test data for main pvacseq test
09e4bae
@susannasiebert
Remove unneeded int castings
db1b663
@susannasiebert
Fix some formatting issues
789237a
@susannasiebert
Skip fusion variants that aren't inframe_fusion or frameshift_fusion
319602c
@susannasiebert
Deduplicate some code
01e33c5
@susannasiebert
Adapt main pipeline to accept INTEGRATE-Neo fusion files
c54aacf
@tmooney tmooney force-pushed the centralize_split_file_path_generation branch from 47a031d to 26ea758 Compare February 7, 2017 15:46
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tmooney commented Feb 7, 2017

I've rebased this again to address accumulated conflicts and added 3ceb7c7.

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