Functions to process, filter, annotate and aggregate variants by transcript expression (get the pext scores per variant) #651

KoalaQin · 2023-12-08T16:18:44Z

Modifications:

change process_consequences, filter_vep_transcript_csqs and preprocess_variants_for_tx to process and filter variants;
move import_gencode into resources_utils.py since it's versatile in any genome build.

Additions:

filter_vep_to_gene_list, import_gencode,  and filter_to_gencode_cds to filter variants;
a few more globals concerning variant consequences in vep.py;
tx_filter_variants_by_csqs, tx_annotate_variants, tx_aggregate_variants and an ensemble function perform_tx_annotation_pipeline to combine the first 3 functions;

…/gnomad_methods into jg/tx_annotate_mt_suggestions # Conflicts: # gnomad/utils/transcript_annotation.py

…ions Suggestions to tx_annotate_mt PR

…adinstitute/gnomad_methods into jg/tx_annotate_mt_suggestions # Conflicts: # gnomad/utils/transcript_annotation.py

…adinstitute/gnomad_methods into jg/tx_annotate_mt_suggestions

…/gnomad_methods into jg/tx_annotate_mt_suggestions # Conflicts: # gnomad/utils/transcript_annotation.py

…ions Suggestions to tx_annotate_mt

gnomad/utils/transcript_annotation.py

jkgoodrich

A few more comments. Also, can you modify the name of the PR and add to the PR description to indicate all the functions that are modified and added? Good example here

gnomad/utils/filtering.py

gnomad/resources/grch38/reference_data.py

gnomad/utils/filtering.py

gnomad/utils/transcript_annotation.py

gnomad/utils/vep.py

jkgoodrich

Just a little bit more

gnomad/resources/grch38/reference_data.py

gnomad/utils/filtering.py

gnomad/utils/vep.py

gnomad/utils/transcript_annotation.py

jkgoodrich

A few smaller things related to naming and doc strings

gnomad/utils/transcript_annotation.py

jkgoodrich · 2024-01-19T22:46:38Z

gnomad/utils/transcript_annotation.py

+    return ht
+
+
+def process_annotate_aggregate_variants(


I think this needs another name. Maybe something like "perform_tx_based_expression_annotation" or "perform_tx_annotation_pipeline", or something else?

How about this new name?

gnomad/utils/vep.py

jkgoodrich

So close! Just a few more suggestions and a couple fixes to the new additions

gnomad/utils/vep.py

gnomad/utils/transcript_annotation.py

gnomad/utils/vep.py

jkgoodrich

One small thing, and can you change the PR description with the updated function names. Then I will approve.

gnomad/utils/vep.py

jkgoodrich

LGTM!

KoalaQin added 2 commits December 8, 2023 09:43

function to annotate variant with transcript expression

77279e8

Aggregate mean_proportion

e9cfeb3

KoalaQin self-assigned this Dec 8, 2023

KoalaQin requested a review from jkgoodrich December 8, 2023 16:18

KoalaQin assigned jkgoodrich Dec 8, 2023

jkgoodrich added the Pext label Dec 14, 2023

KoalaQin added 2 commits December 18, 2023 10:55

merge from base branch

223e130

integrate pull_out_worst_from_tx_annotatate into the main function

373c83e

KoalaQin added the Changelog: new feature label Dec 19, 2023

KoalaQin and others added 21 commits December 18, 2023 20:34

Edit docstring

21b5519

Suggested changes to tx_annotate_variants

0f898e5

Merge branch 'qh/tx_annotate_mt' of /~https://github.com/broadinstitute…

ba3a1c4

…/gnomad_methods into jg/tx_annotate_mt_suggestions # Conflicts: # gnomad/utils/transcript_annotation.py

A little more clean up

9e9a283

Merge pull request #654 from broadinstitute/jg/tx_annotate_mt_suggest…

9e9e60f

…ions Suggestions to tx_annotate_mt PR

merge changes from base branch

1fb32ea

remove redundant content

42714b8

split into small functions: preprocess, annotate and aggregate

5a09617

add TODOs

df86088

add option when 'freq' is not in Table

86852b1

Merge branch 'qh/get_expression_proportion' of /~https://github.com/bro…

81f9106

…adinstitute/gnomad_methods into jg/tx_annotate_mt_suggestions # Conflicts: # gnomad/utils/transcript_annotation.py

Suggestions to tx_annotate_mt

0cf1829

Use process_consequences if ignore_splicing is True

a98fc1f

Fix keep_csqs -> keep_genes

ff26879

Changes from testing

0cac355

Merge branch 'qh/get_expression_proportion' of /~https://github.com/bro…

6957027

…adinstitute/gnomad_methods into jg/tx_annotate_mt_suggestions

Merge branch 'qh/tx_annotate_mt' of /~https://github.com/broadinstitute…

1a1fadb

…/gnomad_methods into jg/tx_annotate_mt_suggestions # Conflicts: # gnomad/utils/transcript_annotation.py

Remove extra tab in docstring

1fdd370

Merge pull request #655 from broadinstitute/jg/tx_annotate_mt_suggest…

0e2aca0

…ions Suggestions to tx_annotate_mt

filter to CDS & redefine grouping

3f0ca81

add CDS filtering in preprocess

a7e791d

apply review suggestions

559c5d8

KoalaQin requested a review from jkgoodrich January 13, 2024 22:40

KoalaQin added 2 commits January 13, 2024 17:46

add gencode v39 resource

6f7cdcb

add tissues to global

e2366ad

KoalaQin commented Jan 15, 2024

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delete annotate tx_ht back to variant ht because key changed

705be2f

jkgoodrich reviewed Jan 16, 2024

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KoalaQin changed the title ~~Function to annotate variant with transcript expression~~ Functions to preprocess, annotate and aggregate variants by transcript expression (get the pext scores) Jan 16, 2024

KoalaQin changed the title ~~Functions to preprocess, annotate and aggregate variants by transcript expression (get the pext scores)~~ Functions to preprocess, annotate and aggregate variants by transcript expression (get the pext scores per variant) Jan 16, 2024

address review comments

6f2a4fb

KoalaQin requested a review from jkgoodrich January 16, 2024 22:04

KoalaQin added 2 commits January 19, 2024 16:16

add warnings to filter_to_cds and option to filter by amino_acids

7ce7eaa

option to filter by valid amino_acids in transcript_consequences

2274f6a

jkgoodrich requested changes Jan 19, 2024

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jkgoodrich reviewed Jan 19, 2024

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jkgoodrich reviewed Jan 19, 2024

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address review comments

aa67ca1

KoalaQin changed the title ~~Functions to preprocess, annotate and aggregate variants by transcript expression (get the pext scores per variant)~~ Functions to process, annotate and aggregate variants by transcript expression (get the pext scores per variant) Jan 19, 2024

KoalaQin changed the title ~~Functions to process, annotate and aggregate variants by transcript expression (get the pext scores per variant)~~ Functions to process, filter, annotate and aggregate variants by transcript expression (get the pext scores per variant) Jan 19, 2024

KoalaQin added 2 commits January 19, 2024 19:07

combine filtering criteria with concatenation

09c3a8e

rename pipeline function

f3764a8

jkgoodrich requested changes Jan 20, 2024

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KoalaQin added 2 commits January 19, 2024 21:44

changes requested by reviewer

baff663

small formatting

7462733

jkgoodrich reviewed Jan 20, 2024

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small formatting * 2

bcbc433

KoalaQin requested a review from jkgoodrich January 20, 2024 03:21

jkgoodrich approved these changes Jan 20, 2024

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KoalaQin merged commit bea49f8 into main Jan 20, 2024
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jkgoodrich deleted the qh/tx_annotate_mt branch January 22, 2024 14:57

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Functions to process, filter, annotate and aggregate variants by transcript expression (get the pext scores per variant) #651

Functions to process, filter, annotate and aggregate variants by transcript expression (get the pext scores per variant) #651

KoalaQin commented Dec 8, 2023 •

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Functions to process, filter, annotate and aggregate variants by transcript expression (get the pext scores per variant) #651

Functions to process, filter, annotate and aggregate variants by transcript expression (get the pext scores per variant) #651

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KoalaQin commented Dec 8, 2023 •

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