Merge dev for release v0.1.1 #9

nebfield · 2022-08-23T15:25:41Z

First proper release of pgscatalog_utils

Using the chromosome causes it to fail if you list of pvar files doesn’t work if there is a chromosome in the scoring file that it’s present in the target. I re-wrote it to loop through pvars instead.

Fix matching

and harmonized files in builds GRCh37/38. Ensures scorefile naming matches the files on the FTP (e.x. PGS002237): - Build = None -> PGS002237.txt.gz - Build = GRCh37 -> PGS002237_hmPOS_GRCh37.txt.gz - Build = GRCh38 -> PGS002237_hmPOS_GRCh38.txt.gz

Adapt download_scorefile to download both author-reported scoring files and harmonized files

…ith missing chromosomal positions or non-standard alleles (e.g. HLA)

…mplex alleles that don't match valid DNA string. Examples: - null -> null - G*06:02 -> G*06:02 - A -> T - AC -> TG - CT -> GA - C -> G - etc.

…clude them)

Keep missing vars

… post-hoc)

…'t be matched

…t pl.concat without diagonal method

use matched_effect_allele

smlmbrt

Made minor edits to the doc strings. These should represent the minimum featureset needed to calculate most PGS within pgsc_calc

nebfield and others added 30 commits August 8, 2022 17:43

download scorefiles with multiple EFO and PGP terms

44c4877

match_variants per chromosome

b620c36

update dependencies

6de8864

add is_multiallelic to log

fad43fd

clean up

dc08ed9

Make the output directory when it doesn't exist

501775e

Refactor the looping of scoring files and target variants:

ceaf91a

Using the chromosome causes it to fail if you list of pvar files doesn’t work if there is a chromosome in the scoring file that it’s present in the target. I re-wrote it to loop through pvars instead.

Merge pull request #3 from PGScatalog/fix_matching

c2bbe3d

Fix matching

Merge branch 'dev' into feat_authorreported

bd4bf10

Update tests

d62586c

Merge remote-tracking branch 'origin/feat_authorreported' into dev

493b7b3

fix tests

26d9252

remove redundant database write

2c4aaf9

Merge pull request #4 from PGScatalog/feat_authorreported

24ee9ec

Adapt download_scorefile to download both author-reported scoring files and harmonized files

check split target chromosomes only contain one chromosome

1141f66

match single target genome variant files iteratively

feb4fd3

tidy up

bff1d09

revert iterative matching on a single file

fdd9b79

fix checking chromosomes

96da74d

Update matching modes

9a832ff

Change default behaviour of combine_scorefiles to not drop variants w…

f5e1c9e

…ith missing chromosomal positions or non-standard alleles (e.g. HLA)

Fix typo

137596c

Update function to complement alleles. Will not complement missing/co…

f4626f2

…mplex alleles that don't match valid DNA string. Examples: - null -> null - G*06:02 -> G*06:02 - A -> T - AC -> TG - CT -> GA - C -> G - etc.

Fix regex to 1 or more from zero or more

3e43c8f

Suggested argument to ignore strand_flips (default behaviour is to in…

369a69a

…clude them)

Flip scorefile instead of target data

fd382af

get best match type

b926d2d

move debug statement

b5c8531

match with complemented scorefile columns instead of target columns

b2bc27c

nebfield and others added 22 commits August 16, 2022 14:13

fix liftover with missing positions

7859ef7

skip flips with parameter

f2a2194

Merge pull request #6 from PGScatalog/keep_missing_vars

8f3302c

Keep missing vars

fix matches, and be clearer about match keys

1a814dc

fix matching with flipped alleles

4e13ebb

update labelling biallelic ambiguous variants

a373f0a

update assert

0030856

Edit description

1bcc2d0

Ignore strand flips by not looking for them (instead of dropping them…

d3e0f69

… post-hoc)

Ignore variants with null positional data (e.g. HLA alleles) that can…

95eaad7

…'t be matched

Backfill REF/ALT alleles in matches, and reorder columns for efficien…

4d53823

…t pl.concat without diagonal method

.select() is faster than [] on large pl.DataFrames

8888a1f

fix handling matches without other allele

eba42d0

add test cases

4071a88

skip scoring files that fail matching, unless no files match

dde95a7

don't check target chroms in fast match mode

cf3a3d6

fix fill_null

3ea552f

Merge pull request #7 from PGScatalog/match_nicer

e5937d3

use matched_effect_allele

remove redundant function

3662ed8

bump version

64289e5

Citation edits

309fcf5

update descriptions in args

c8ef7c9

nebfield requested a review from smlmbrt August 23, 2022 15:25

Minor description edits

50999ac

smlmbrt approved these changes Aug 23, 2022

View reviewed changes

smlmbrt merged commit c1b5290 into main Aug 23, 2022

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Merge dev for release v0.1.1 #9

Merge dev for release v0.1.1 #9

nebfield commented Aug 23, 2022 •

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Merge dev for release v0.1.1 #9

Merge dev for release v0.1.1 #9

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nebfield commented Aug 23, 2022 •

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