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Conpair concordance: account for different format when run with --outfile #1855

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merged 8 commits into from Aug 30, 2023

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ehenrion
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@ehenrion ehenrion commented Feb 2, 2023

  • Update of the search pattern for conpair/concordance to match with all types of Conpair outputs.
  • Update of the conpair.py module to parse concordance metrics from all types of Conpair outputs.
  • CHANGELOG.md has been updated

@vladsavelyev
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vladsavelyev commented Aug 11, 2023

I think the PR looks great. It would be nice to add tests for this into https://github.com/ewels/MultiQC_TestData, it should be good to merge?

@vladsavelyev vladsavelyev added awaits-review Awaiting final review and merge. waiting: response Waiting for more information from user and removed awaits-review Awaiting final review and merge. labels Aug 30, 2023
vladsavelyev added a commit to MultiQC/test-data that referenced this pull request Aug 30, 2023
vladsavelyev added a commit to MultiQC/test-data that referenced this pull request Aug 30, 2023
@vladsavelyev vladsavelyev changed the title Conpair concordance : update of conpair.py and search_patterns.yaml Conpair concordance: account for different format when run with --outfile Aug 30, 2023
@vladsavelyev vladsavelyev merged commit d783223 into MultiQC:master Aug 30, 2023
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Apparently I started but never submitted a review on this in... February 😓

I'll put in a follow-up PR to address at least the float thing.

multiqc/modules/conpair/conpair.py Show resolved Hide resolved
if match:
parsed_data[k] = float(match.group(1))
if k == "concordance_concordance" and not "Concordance" in r:
parsed_data[k] = 100 * parsed_data[k]
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Force float variable type, otherwise we get weird integer problems..

Suggested change
parsed_data[k] = 100 * parsed_data[k]
parsed_data[k] = 100.0 * float(parsed_data[k])

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3 participants