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feat: plink2 support #67

Merged
merged 30 commits into from
Jul 20, 2022
Merged

feat: plink2 support #67

merged 30 commits into from
Jul 20, 2022

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aryarm
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@aryarm aryarm commented Jul 20, 2022 •
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This PR adds experimental support for PLINK2 PGEN files in the transform and simphenotype subcommands.

It also adds documentation for the classes in the data module and thus, closes #50.

aryarm added 30 commits June 24, 2022 16:13
@aryarm
start on docs page for data.Genotypes and data.Haplotypes
0735e74 
see #50
@aryarm
add a GenotypesPLINK.__iter__() method
e745915
@aryarm
add temp GenotypesPLINK.write() method
e0aeba6
@aryarm
add chunk_size param to GenotypesPLINK.read()
d553e0c
@aryarm
create script for benchmarking genotype readers
7139929
@aryarm
handle uneven chunk sizes in GenotypesPLINK.read()
f2f9b1b
@aryarm
benchmark genotypes with more variants
373d9da
@aryarm
test GenotypesPLINK class
e568db4
@aryarm
allow str or Path fnames for classes in the data module
ba487df
@aryarm
add support for pgen files in transform subcommand
36c537f
@aryarm
skip TestGenotypesPLINK if pgenlib can't be imported
437fadd
@aryarm
add slope to benchmarking plot
6ccf9b2
@aryarm
add options to discard missing genotypes and subset haplotypes in tra…
b7964b7 
…nsform subcommand
@aryarm
move global vars into params in benchmarking script
901e299
@aryarm
add chunk_size param to transform subcommand
fbe56d9
@aryarm
update lock file to pysam 0.19.1
4be25fa
@aryarm
update to pysam v0.19.1 to avoid pysam-developers/pysam#1104
8efd9a7
@aryarm
move chunk_size param to GenotypesPLINK.__init__
e0446a3
@aryarm
support writing PLINK2 files
cd7e6e1
@aryarm
skip plink2 write tests when pgenlib isn't installed
ebf2155
@aryarm
try benchmarking with PLINK2 with UKB
2542fbb
@aryarm
describe how to use GenotypesPLINK class in data docs
2bbe43d
@aryarm
Merge branch 'docs/data' into feat/plink2
2d2b9e9
@aryarm
warn if pgenlib is not installed
8185ea3
@aryarm
document support for reading and writing pgen files in transform
3add451
@aryarm
document GenotypesPLINK.read_variants and GenotypesPLINK.read_samples
cca85a8
@aryarm
finish creating plot for benchmarking PGEN vs VCF
83b7285
@aryarm
make sure to close the pgen file after writing
1e2a8cb
@aryarm
add phenotypes and covariates section to data docs
2b50784
@aryarm
add support for PGEN files to the simphenotype command
984708a
@aryarm aryarm merged commit c8a7773 into main Jul 20, 2022
@aryarm aryarm deleted the feat/plink2 branch July 20, 2022 05:22
@aryarm aryarm mentioned this pull request Jul 20, 2022
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documentation for the data module
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@aryarm