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update dataset file lookup

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rdk
2025-08-23 19:00:47 +02:00
parent 7c1f389979
commit 634c9fd92e
2 changed files with 24 additions and 18 deletions
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4
config/pept/pept.groovy
View File

@@ -9,13 +9,13 @@ import cz.siret.prank.program.params.Params
* define this if you want dataset program parameters to be evaluated relative to this directory
* (set absolute path or path relative to install dir, null defaults to working dir)
*/
dataset_base_dir = "../../p2rank-pept-data/peptides/sprint17"
dataset_base_dir = "../../../p2rank-pept-data/peptides/sprint17"
/**
* all output of the program will be stored in subdirectories of this directory
* (set absolute path or path relative to install dir, null defaults to working dir)
*/
output_base_dir = "../../p2rank-pept-results/${version}"
output_base_dir = "../../../p2rank-pept-results/${version}"
predict_residues = true

38
src/main/groovy/cz/siret/prank/program/Main.groovy
View File

@@ -104,8 +104,9 @@ class Main implements Parametrized, Writable {
lastConfigPath = fcustom.absolutePath
}
params.dataset_base_dir = evalDirParam(params.dataset_base_dir, Futils.dir(lastConfigPath))
params.output_base_dir = evalDirParam(params.output_base_dir, Futils.dir(lastConfigPath))
String lastConfigDir = Futils.dir(lastConfigPath)
params.dataset_base_dir = evalDirParam(params.dataset_base_dir, lastConfigDir)
params.output_base_dir = evalDirParam(params.output_base_dir, lastConfigDir)
params.updateFromCommandLine(args)
if (args.hasNamedArg("dataset_base_dir")) {
@@ -132,23 +133,23 @@ class Main implements Parametrized, Writable {
log.debug "CMD LINE ARGS: " + args
}
String evalDirParam(String dir, String relativePrefixDir) {
if (dir == null) {
dir = "."
String evalDirParam(String dirParam, String relativePrefixDir) {
if (dirParam == null) {
dirParam = "."
} else {
if (!new File(dir).isAbsolute()) {
dir = "$relativePrefixDir/$dir"
if (!Futils.isAbsolute(dirParam)) {
dirParam = "$relativePrefixDir/$dirParam"
}
}
write "DIR: $dir"
write "DIR: $dirParam"
dir = dir.replace("{version}", version)
dirParam = dirParam.replace("{version}", version)
write "DIR2: $dir"
write "DIR2: $dirParam"
dir = Futils.absPath(Futils.normalize(dir))
return dir
dirParam = Futils.absPath(Futils.normalize(dirParam))
return dirParam
}
static String findModel(String installDir, Params params) {
@@ -174,11 +175,16 @@ class Main implements Parametrized, Writable {
throw new PrankException('dataset not specified!')
}
if (!Futils.exists(dataf)) {
log.info "looking for dataset in working dir [${Futils.absPath(dataf)}]... failed"
dataf = "${Params.inst.dataset_base_dir}/$dataf"
if (Futils.isAbsolute(dataf)) {
log.info "using provided absolute path to the dataset [${dataf}]"
return dataf
}
if (!Futils.exists(dataf)) {
log.info "looking for the dataset in working dir [${Futils.absPath(dataf)}] failed"
dataf = "${Params.inst.dataset_base_dir}/$dataf"
log.info "looking for the dataset in dataset_base_dir [${Futils.absPath(dataf)}]..."
}
log.info "looking for dataset in dataset_base_dir [${Futils.absPath(dataf)}]..."
return dataf
}