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Add Bed Classifier #35

Merged
merged 13 commits into from
Feb 14, 2024
Merged

Add Bed Classifier #35

merged 13 commits into from
Feb 14, 2024

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donaldcampbelljr
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@donaldcampbelljr donaldcampbelljr commented Feb 12, 2024 •
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Addresses #34

@donaldcampbelljr donaldcampbelljr changed the base branch from dev_phc_bed_Metadata to dev February 13, 2024 21:25
@donaldcampbelljr donaldcampbelljr marked this pull request as ready for review February 13, 2024 21:26
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Currently, this is classifying narrowPeak or broadPeak if it has the proper number of columns AND narrowPeak or broadPeak is in the sample name. It is not relying on column names as these are sometimes not provided.

Other classifications are of the form: "bed3+6", "bed4+8" etc.

Finally, if classification cannot be determined: "unknown_bedtype"

khoroshevskyi
khoroshevskyi requested changes Feb 14, 2024
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There are few lines of code that should be fixed

bedboss/bedclassifier/bedclassifier.py Outdated Show resolved Hide resolved
test/test_bedclassifier.py Outdated Show resolved Hide resolved
test/test_bedclassifier.py Outdated Show resolved Hide resolved
khoroshevskyi
khoroshevskyi approved these changes Feb 14, 2024
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LGTM

@khoroshevskyi khoroshevskyi merged commit b23c0a7 into dev Feb 14, 2024
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@khoroshevskyi khoroshevskyi deleted the dev_assign_bed_format branch February 14, 2024 18:01
@nsheff nsheff added this to the v0.1.0 milestone Feb 16, 2024
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@khoroshevskyi khoroshevskyi khoroshevskyi approved these changes

@nsheff nsheff Awaiting requested review from nsheff

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@donaldcampbelljr @khoroshevskyi @nsheff