LDpred2/createBackingFile.R: process .bgen files (#200)

* `LDpred2/createBackingFile.R`: support BGEN file format
Fixes #199

* test works

* bumped version.py to 1.3.7

* changed date

CHANGELOG.md

@@ -39,6 +39,12 @@ If MD5 sum is not listed for a certain release then it means that the container
 
 * Miscellaneous goes here
 
+## [1.3.7] - 2023-10-17
+
+### Added
+
+* Added a feature to read and convert BGEN (.bgen) files to ``scripts/pgs/LDpred2/createBackingFile.R``
+
 ## [1.3.6] - 2023-08-17
 
 ### Fixed

scripts/pgs/LDpred2/createBackingFile.R

@@ -3,9 +3,10 @@
 library(bigsnpr, quietly = T)
 library(tools)
 library(argparser, quietly=T)
-par <- arg_parser('Create bigSNPR rds/bk (backing) files from plink bed files')
-par <- add_argument(par, 'file-input', help='The bed input file')
+par <- arg_parser('Create bigSNPR rds/bk (backing) files from PLINK (.bed) or BGEN (.bgen)) files')
+par <- add_argument(par, 'file-input', help='The input file (.bed/.bgen file ending)')
 par <- add_argument(par, 'file-output', help='The output basename of files')
+par <- add_argument(par, '--file-snp-list', help='Text file containing list of SNPs to extract from .bgen file (format <chr>_<pos>_<a1>_<a2>)', default = NULL)
 parsed <- parse_args(par)
 if (!file.exists(parsed$file_input)) stop(parsed$file_input, ' does not exist!')
 # If the user passes a file.rds, the output will not be file.rds.rds
@@ -18,5 +19,12 @@ if (file.exists(outputFileRDS)) {
   quit('no') # Exit without saving the workspace
 }
 cat('Processing', parsed$file_input, '\n')
-res <- snp_readBed(parsed$file_input, backingfile = baseName)
+file_ext = tolower(file_ext(parsed$file_input))
+if (file_ext == 'bed') {
+  res <- snp_readBed(parsed$file_input, backingfile = baseName)
+} else if (file_ext == 'bgen') {
+  res <- snp_readBGEN(parsed$file_input, backingfile = baseName, list_snp_id = list(scan(parsed$file_snp_list, character())))
+} else {
+  stop('Unknown file extension: ', file_ext)
+}
 cat('Created', baseName, ' (.rds, .bk)\n')

tests/test_LDpred2/run.sh

@@ -30,6 +30,15 @@ export fileOutputSNPR=$DIR_DATA/public-data3.rds
 export fileKeepSNPS=/REF/hapmap3/w_hm3.justrs
 export fileOut=$DIR_TESTS/output/public-data.score
 
+# BGEN files
+export fileBGEN=$DIR_DATA/example.bgen
+export fileBGENasRDS=$DIR_DATA/example.rds
+export fileSNPlist=$DIR_DATA/example.snps
+
+# copy .bgen files
+cp $DIR_REFERENCE/examples/regenie/example.bgen $fileBGEN
+cp $DIR_REFERENCE/examples/regenie/example.bgen.bgi $fileBGEN.bgi
+
 ### For imputation testing
 # Copy some plink files
 cp $DIR_REFERENCE/examples/prsice2/EUR.bed $DIR_DATA/
@@ -40,9 +49,10 @@ fileImpute=$DIR_DATA/EUR
 # Imputed file
 fileImputed=$DIR_DATA/EUR_imputed
 
-
 # Create shortcut environment variable for Rscript 
 export RSCRIPT="singularity exec -B $DIR_BASE:$DIR_BASE -B $DIR_REF_LDPRED:/ldpred2_ref -B $DIR_REFERENCE:/REF $DIR_SIF/r.sif Rscript"
+export BGENIX="singularity exec -B $DIR_BASE:$DIR_BASE -B $DIR_REF_LDPRED:/ldpred2_ref -B $DIR_REFERENCE:/REF $DIR_SIF/gwas.sif bgenix"
+export PYTHON="singularity exec -B $DIR_BASE:$DIR_BASE -B $DIR_REF_LDPRED:/ldpred2_ref -B $DIR_REFERENCE:/REF $DIR_SIF/python3.sif python"
 
 # The different modes to run (affects runs of scripts/extended.sh)
 LDPRED_MODES="inf auto"

tests/test_LDpred2/scripts/backingfile.sh

@@ -9,3 +9,11 @@ if [ $? -eq 1 ]; then echo "$dump"; exit; fi
 
 dump=$( $RSCRIPT $DIR_SCRIPTS/createBackingFile.R $fileInputGeno $fileOutputSNPR )
 if [ $? -eq 1 ]; then echo "$dump"; exit; fi
+
+# check that .bgen file can be converted
+# First, create data/snp_list_id.txt file
+dump=$( $BGENIX -g $fileBGEN -incl-range 1:0- -list > $fileSNPlist )
+dump=$( $PYTHON -c "import os; import pandas as pd; df = pd.read_csv('$fileSNPlist', delim_whitespace=True, skipfooter=1, skiprows=[0], engine='python'); df = df[['chromosome', 'position', 'first_allele', 'alternative_alleles']]; df.to_csv('$fileSNPlist', index=False, sep='_', header=False)" )
+# Then, create backing file
+dump=$( $RSCRIPT $DIR_SCRIPTS/createBackingFile.R $fileBGEN $fileBGENasRDS --file-snp-list $fileSNPlist )
+if [ $? -eq 1 ]; then echo "$dump"; exit; fi

version/version.py

@@ -2,7 +2,7 @@
 _MINOR = "3"
 # On main and in a nightly release the patch should be one ahead of the last
 # released build.
-_PATCH = "6"
+_PATCH = "7"
 # This is mainly for nightly builds which have the suffix ".dev$DATE". See
 # https://semver.org/#is-v123-a-semantic-version for the semantics.
 _SUFFIX = ""