prstools 0.0.76__tar.gz → 0.0.78__tar.gz

{prstools-0.0.76/prstools.egg-info → prstools-0.0.78}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: prstools
-Version: 0.0.76
+Version: 0.0.78
 Summary: Convenient and powerfull Polygenic Risk Score creation.
 Home-page: https://github.com/mennojw/prstools-release
 Author: Menno Witteveen et al.
@@ -43,7 +43,7 @@ Requires-Dist: seaborn; extra == "full"
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
 
 `prstools` is software to create Polygenic Risk Scores (PRS) directly
-from the commandline <br> (and optionally from inside python).
+from the commandline. <br>
 
 It makes PRS generation easier, compared to previous tools, by:
 
@@ -94,62 +94,40 @@ prstools prscs2 --ref ldref_1kg_pop --target target \
 This will run PRS-CS2 on the example data, using the new implementation
 to demonstrate the capabilities of `prstools` and makes PRS predictions
 for the example dataset. The best and fastest way to get a PRS for your
-is to try the **Tutorial** below. <br> There is also the `prstools`
-documentation, which resides inside of the command-line interface, which
-you can see by typing `prstools`.
-
-``` console
-Usage:
- prstools <command> ...
-
-Convenient and powerfull Polygenic Risk Score creation. 
-'prst' is a commandline shorthand for 'prstools'
-
-Models & Utility Commands:
- <command>
-  downloadutil  Download and unpack LD reference panels and other data.
-  combine       A tool to combine genetics-related text files.
-  prscs2        PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes
-                under continuous shrinkage (CS) priors.
-```
+case is to try the **Tutorial** below. <br>
 
-By combining `prstools` with another `<command>` a specific model or
-other functionality can be used. <br> Forinstance typing
-`prstools prscs2` will output the **documentation** for the prscs2
-subcommand:
+There is also the `prstools` documentation, residing inside of the
+command-line interface, which you can see by typing `prstools` or a
+subcommand. <br> Forinstance typing `prstools prscs2` will output the
+**documentation** for the `prscs2` subcommand:
 
-``` console
-Usage:
- prstools prscs2 [-h  --cpus <number-of-cpus>] --ref <dir/refcode> --target <bim-prefix>
+    Usage:
+     prst prscs2 [-h  --cpus <num-of-cpus>] --ref <dir/refcode> --target <bim-prefix>
                        --sst <file> --out <dir+prefix> [--n_gwas <num>  --chrom <chroms>]
-                       [--colmap <alternative_colnames>  --pred  --n_iter <n_iter>]
-                       [--n_burnin <n_burnin>  --n_slice <n_slice>  --seed <seed>  --a <a>]
-                       [--b <b>  --phi <phi>  --clip <clip>  --sampler <sampler>]
-
-PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes under continuous shrinkage (CS) priors.
+                       [--colmap <colnames>  --rsidmode <yes/no>  --pred <yes/no>]
+                       [--n_iter <n_iter>  --n_burnin <n_burnin>  --n_slice <n_slice>]
+                       [--seed <seed>  --a <a>  --b <b>  --phi <phi>  --clip <clip>]
+                       [--sampler <sampler>  --n_jobs <n_jobs>]
 
-General Options:
- -h, --help                               Show this help message and exit.
- -c, --cpus <number-of-cpus>              The number of cpus to use. Generally most efficient if
-                                          chosen to be between 1 and 5. Functionality can be
+    PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes under 
+    continuous shrinkage (CS) priors.
 
-... [omitted for readability] ...
+    General Options:
+     -h, --help                 Show this help message and exit.
 
+    ... [omitted for readability] ...
 
- --clip <clip>                            Clip parameter. The default works best in pretty much
-                                          all cases. (default: 1.0)
- --sampler <sampler>                      Sampler algorithm. Rue sampling is the original sampler,
-                                          which gives good results. (default: Rue)
+     --n_jobs <n_jobs>          This sets the number of jobs for parallel processing. (default:
+                                8)
 
-Examples --> can be directly copy-pasted (:
- prst downloadutil --pattern example --destdir ./; cd example                                                # Makes 'example' dir in current path.
- prstools prscs2 --ref ldref_1kg_pop --target target --sst sumstats.tsv --n_gwas 2565 --out ./result-prscs2 # Run the model with example data.
- prst prscs2 -r ldref_1kg_pop -t target -s sumstats.tsv -n 2565 -o ./result-prscs2 --pred                  # A shorter version of previous that also does the predictions.
-```
+    # Examples (get data, run model) --> can be directly copy-pasted (:
+    prstools downloadutil --pattern example --destdir ./; cd example        
+    prst prscs2 --ref ldref_1kg_pop -t target -s sumstats.tsv --n_gwas 2565 --out result-prscs2
 
 As can be seen, there are examples at the end of the help output to
-illustrate usage, which should work with a simple copy-paste. There is
-now also an online version of all this documentation
+illustrate usage, which should work with a simple copy-paste.
+
+There is now also an online version of all this documentation
 (https://prstools.readthedocs.io/). <br>
 
 ## Tutorial + Video

{prstools-0.0.76 → prstools-0.0.78}/README.md

@@ -4,7 +4,7 @@
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
 
 `prstools` is software to create Polygenic Risk Scores (PRS) directly
-from the commandline <br> (and optionally from inside python).
+from the commandline. <br>
 
 It makes PRS generation easier, compared to previous tools, by:
 
@@ -55,62 +55,40 @@ prstools prscs2 --ref ldref_1kg_pop --target target \
 This will run PRS-CS2 on the example data, using the new implementation
 to demonstrate the capabilities of `prstools` and makes PRS predictions
 for the example dataset. The best and fastest way to get a PRS for your
-is to try the **Tutorial** below. <br> There is also the `prstools`
-documentation, which resides inside of the command-line interface, which
-you can see by typing `prstools`.
-
-``` console
-Usage:
- prstools <command> ...
-
-Convenient and powerfull Polygenic Risk Score creation. 
-'prst' is a commandline shorthand for 'prstools'
-
-Models & Utility Commands:
- <command>
-  downloadutil  Download and unpack LD reference panels and other data.
-  combine       A tool to combine genetics-related text files.
-  prscs2        PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes
-                under continuous shrinkage (CS) priors.
-```
+case is to try the **Tutorial** below. <br>
 
-By combining `prstools` with another `<command>` a specific model or
-other functionality can be used. <br> Forinstance typing
-`prstools prscs2` will output the **documentation** for the prscs2
-subcommand:
+There is also the `prstools` documentation, residing inside of the
+command-line interface, which you can see by typing `prstools` or a
+subcommand. <br> Forinstance typing `prstools prscs2` will output the
+**documentation** for the `prscs2` subcommand:
 
-``` console
-Usage:
- prstools prscs2 [-h  --cpus <number-of-cpus>] --ref <dir/refcode> --target <bim-prefix>
+    Usage:
+     prst prscs2 [-h  --cpus <num-of-cpus>] --ref <dir/refcode> --target <bim-prefix>
                        --sst <file> --out <dir+prefix> [--n_gwas <num>  --chrom <chroms>]
-                       [--colmap <alternative_colnames>  --pred  --n_iter <n_iter>]
-                       [--n_burnin <n_burnin>  --n_slice <n_slice>  --seed <seed>  --a <a>]
-                       [--b <b>  --phi <phi>  --clip <clip>  --sampler <sampler>]
-
-PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes under continuous shrinkage (CS) priors.
+                       [--colmap <colnames>  --rsidmode <yes/no>  --pred <yes/no>]
+                       [--n_iter <n_iter>  --n_burnin <n_burnin>  --n_slice <n_slice>]
+                       [--seed <seed>  --a <a>  --b <b>  --phi <phi>  --clip <clip>]
+                       [--sampler <sampler>  --n_jobs <n_jobs>]
 
-General Options:
- -h, --help                               Show this help message and exit.
- -c, --cpus <number-of-cpus>              The number of cpus to use. Generally most efficient if
-                                          chosen to be between 1 and 5. Functionality can be
+    PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes under 
+    continuous shrinkage (CS) priors.
 
-... [omitted for readability] ...
+    General Options:
+     -h, --help                 Show this help message and exit.
 
+    ... [omitted for readability] ...
 
- --clip <clip>                            Clip parameter. The default works best in pretty much
-                                          all cases. (default: 1.0)
- --sampler <sampler>                      Sampler algorithm. Rue sampling is the original sampler,
-                                          which gives good results. (default: Rue)
+     --n_jobs <n_jobs>          This sets the number of jobs for parallel processing. (default:
+                                8)
 
-Examples --> can be directly copy-pasted (:
- prst downloadutil --pattern example --destdir ./; cd example                                                # Makes 'example' dir in current path.
- prstools prscs2 --ref ldref_1kg_pop --target target --sst sumstats.tsv --n_gwas 2565 --out ./result-prscs2 # Run the model with example data.
- prst prscs2 -r ldref_1kg_pop -t target -s sumstats.tsv -n 2565 -o ./result-prscs2 --pred                  # A shorter version of previous that also does the predictions.
-```
+    # Examples (get data, run model) --> can be directly copy-pasted (:
+    prstools downloadutil --pattern example --destdir ./; cd example        
+    prst prscs2 --ref ldref_1kg_pop -t target -s sumstats.tsv --n_gwas 2565 --out result-prscs2
 
 As can be seen, there are examples at the end of the help output to
-illustrate usage, which should work with a simple copy-paste. There is
-now also an online version of all this documentation
+illustrate usage, which should work with a simple copy-paste.
+
+There is now also an online version of all this documentation
 (https://prstools.readthedocs.io/). <br>
 
 ## Tutorial + Video

{prstools-0.0.76 → prstools-0.0.78}/prstools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.0.76"
+__version__ = "0.0.78"
 _date = "22-09-2026"
 
 import importlib as _importlib

{prstools-0.0.76 → prstools-0.0.78}/prstools/_parser_vars.py

@@ -150,8 +150,8 @@ def get_subparserkwg_lst():
       'display_info': True,
       'help': 'PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes under continuous shrinkage (CS) priors.',
       'epilog': '\x1b[32m# Examples (get data, run model) --> can be directly copy-pasted (:\x1b[0m\n'
-                'prst downloadutil --pattern example --destdir ./; cd example        \n'
-                'prstools prscs2 --ref ldref_1kg_pop -t target --sst sumstats.tsv --n_gwas 2565 --out ./result-prscs2\n',
+                'prstools downloadutil --pattern example --destdir ./; cd example        \n'
+                'prst prscs2 --ref ldref_1kg_pop -t target -s sumstats.tsv --n_gwas 2565 --out result-prscs2\n',
       'modulename': 'prstools.models._base',
       'groups': {'general': {'grpheader': 'General Options',
                              'pkwargs': {'basics': {'args': ['-h', '--help'], 'kwargs': {'action': 'help', 'help': 'Show this help message and exit.'}},

{prstools-0.0.76 → prstools-0.0.78}/prstools/models/_base.py

@@ -87,8 +87,8 @@ class BasePred(ABC):
         
         epilog=f'''\
         # Examples (get data, run model) --> can be directly copy-pasted (:
-        prst downloadutil --pattern example --destdir ./; cd example  {insert}
-        prstools {cmdname} --ref {ldrefname} -t target --sst sumstats.tsv {chromopt}--n_gwas 2565 --out ./result-{cmdname}
+        prstools downloadutil --pattern example --destdir ./; cd example  {insert}
+        prst {cmdname} --ref {ldrefname} -t target -s sumstats.tsv {chromopt}--n_gwas 2565 --out result-{cmdname}
         '''
         
         # prst {cmdname} -r {ldrefname} -t target -s sumstats.tsv -n 2565 {chromopt}-o ./result-{cmdname} --pred # A shorter version of previous that also does the predictions.
@@ -209,7 +209,7 @@ class BasePred(ABC):
         return pkwargs
     
     @classmethod
-    def _get_linkageclass(pkwargs=None, ref=None):
+    def _get_linkageclass(cls, pkwargs=None, ref=None):
         if pkwargs is None: pkwargs = cls._get_pkwargs_for_class(cls)
         try: from prstools.linkage import AutoLinkageData as linkcls
         except: from prstools.linkage import RefLinkageData as linkcls
@@ -246,11 +246,11 @@ class BasePred(ABC):
         if pred and pred != 'no': # Prediction
             try: 
                 bed = prst.io.load_bed(target, verbose=verbose);
-                yhat = model.predict(bed, rsidmode=rsidmode) 
+                yhat = model.predict(bed, rsidmode=rsidmode)
                 prst.io.save_prs(yhat, fn=out_fnfmt, verbose=verbose); ysv=True  # Store prediction result (ysv is helper var, to see if step finished)
-                pheno = prst.io.load_pheno(target, verbose=verbose)
-                scores = prst.scores.eval(pheno, yhat, metrics=['R2','AUC','etc'], verbose=verbose)
-                prst.io.save_scores(scores, fn=out_fnfmt, verbose=verbose)
+                #pheno = prst.io.load_pheno(target, verbose=verbose)
+                #scores = prst.scores.eval(pheno, yhat, metrics=['R2','AUC','etc'], verbose=verbose)
+                #prst.io.save_scores(scores, fn=out_fnfmt, verbose=verbose)
             except Exception as e: # One could have some remarks about the logic of this section, but Menno did not want an if/else jungle here.
                 inject = 'evaluation' if ysv else 'prediction'
                 msg = (f"Could not generate {inject} (e.g. plink/pheno file missing)" 

{prstools-0.0.76 → prstools-0.0.78/prstools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: prstools
-Version: 0.0.76
+Version: 0.0.78
 Summary: Convenient and powerfull Polygenic Risk Score creation.
 Home-page: https://github.com/mennojw/prstools-release
 Author: Menno Witteveen et al.
@@ -43,7 +43,7 @@ Requires-Dist: seaborn; extra == "full"
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
 
 `prstools` is software to create Polygenic Risk Scores (PRS) directly
-from the commandline <br> (and optionally from inside python).
+from the commandline. <br>
 
 It makes PRS generation easier, compared to previous tools, by:
 
@@ -94,62 +94,40 @@ prstools prscs2 --ref ldref_1kg_pop --target target \
 This will run PRS-CS2 on the example data, using the new implementation
 to demonstrate the capabilities of `prstools` and makes PRS predictions
 for the example dataset. The best and fastest way to get a PRS for your
-is to try the **Tutorial** below. <br> There is also the `prstools`
-documentation, which resides inside of the command-line interface, which
-you can see by typing `prstools`.
-
-``` console
-Usage:
- prstools <command> ...
-
-Convenient and powerfull Polygenic Risk Score creation. 
-'prst' is a commandline shorthand for 'prstools'
-
-Models & Utility Commands:
- <command>
-  downloadutil  Download and unpack LD reference panels and other data.
-  combine       A tool to combine genetics-related text files.
-  prscs2        PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes
-                under continuous shrinkage (CS) priors.
-```
+case is to try the **Tutorial** below. <br>
 
-By combining `prstools` with another `<command>` a specific model or
-other functionality can be used. <br> Forinstance typing
-`prstools prscs2` will output the **documentation** for the prscs2
-subcommand:
+There is also the `prstools` documentation, residing inside of the
+command-line interface, which you can see by typing `prstools` or a
+subcommand. <br> Forinstance typing `prstools prscs2` will output the
+**documentation** for the `prscs2` subcommand:
 
-``` console
-Usage:
- prstools prscs2 [-h  --cpus <number-of-cpus>] --ref <dir/refcode> --target <bim-prefix>
+    Usage:
+     prst prscs2 [-h  --cpus <num-of-cpus>] --ref <dir/refcode> --target <bim-prefix>
                        --sst <file> --out <dir+prefix> [--n_gwas <num>  --chrom <chroms>]
-                       [--colmap <alternative_colnames>  --pred  --n_iter <n_iter>]
-                       [--n_burnin <n_burnin>  --n_slice <n_slice>  --seed <seed>  --a <a>]
-                       [--b <b>  --phi <phi>  --clip <clip>  --sampler <sampler>]
-
-PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes under continuous shrinkage (CS) priors.
+                       [--colmap <colnames>  --rsidmode <yes/no>  --pred <yes/no>]
+                       [--n_iter <n_iter>  --n_burnin <n_burnin>  --n_slice <n_slice>]
+                       [--seed <seed>  --a <a>  --b <b>  --phi <phi>  --clip <clip>]
+                       [--sampler <sampler>  --n_jobs <n_jobs>]
 
-General Options:
- -h, --help                               Show this help message and exit.
- -c, --cpus <number-of-cpus>              The number of cpus to use. Generally most efficient if
-                                          chosen to be between 1 and 5. Functionality can be
+    PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes under 
+    continuous shrinkage (CS) priors.
 
-... [omitted for readability] ...
+    General Options:
+     -h, --help                 Show this help message and exit.
 
+    ... [omitted for readability] ...
 
- --clip <clip>                            Clip parameter. The default works best in pretty much
-                                          all cases. (default: 1.0)
- --sampler <sampler>                      Sampler algorithm. Rue sampling is the original sampler,
-                                          which gives good results. (default: Rue)
+     --n_jobs <n_jobs>          This sets the number of jobs for parallel processing. (default:
+                                8)
 
-Examples --> can be directly copy-pasted (:
- prst downloadutil --pattern example --destdir ./; cd example                                                # Makes 'example' dir in current path.
- prstools prscs2 --ref ldref_1kg_pop --target target --sst sumstats.tsv --n_gwas 2565 --out ./result-prscs2 # Run the model with example data.
- prst prscs2 -r ldref_1kg_pop -t target -s sumstats.tsv -n 2565 -o ./result-prscs2 --pred                  # A shorter version of previous that also does the predictions.
-```
+    # Examples (get data, run model) --> can be directly copy-pasted (:
+    prstools downloadutil --pattern example --destdir ./; cd example        
+    prst prscs2 --ref ldref_1kg_pop -t target -s sumstats.tsv --n_gwas 2565 --out result-prscs2
 
 As can be seen, there are examples at the end of the help output to
-illustrate usage, which should work with a simple copy-paste. There is
-now also an online version of all this documentation
+illustrate usage, which should work with a simple copy-paste.
+
+There is now also an online version of all this documentation
 (https://prstools.readthedocs.io/). <br>
 
 ## Tutorial + Video

{prstools-0.0.76 → prstools-0.0.78}/settings.ini

@@ -1,7 +1,7 @@
 [DEFAULT]
 repo = prstools
 lib_name = prstools
-version = 0.0.76
+version = 0.0.78
 min_python = 3.8
 license = mit
 black_formatting = False