pheval-exomiser 0.2.3__tar.gz → 0.2.4__tar.gz

{pheval_exomiser-0.2.3 → pheval_exomiser-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pheval_exomiser
-Version: 0.2.3
+Version: 0.2.4
 Summary: 
 Author: Yasemin Bridges
 Author-email: y.bridges@qmul.ac.uk
@@ -16,7 +16,7 @@ Requires-Dist: google (>=3.0.0,<4.0.0)
 Requires-Dist: oaklib (>=0.5.12,<0.6.0)
 Requires-Dist: pandas (>=1.5.2,<2.0.0)
 Requires-Dist: phenopackets (>=2.0.2,<3.0.0)
-Requires-Dist: pheval (>=0.3.1,<0.4.0)
+Requires-Dist: pheval (>=0.4.0,<0.5.0)
 Requires-Dist: pyaml (>=21.10.1,<22.0.0)
 Requires-Dist: pydantic (>=1.10.7,<2.0.0)
 Description-Content-Type: text/markdown
@@ -27,7 +27,13 @@ This is the Exomiser plugin for PhEval. With this plugin, you can leverage the v
 
 ## Installation
 
-Clone the pheval.exomiser repo and set up the poetry environment:
+You can install the Exomiser directly with PyPi (recommended):
+
+```shell
+pip install pheval.exomiser
+```
+
+Alternatively you can clone the pheval.exomiser repo and set up the poetry environment:
 
 ```shell
 git clone https://github.com/monarch-initiative/pheval.exomiser.git
@@ -80,6 +86,8 @@ The analysis configuration file (in this case: `preset-exome-analysis.yml`) shou
 
 The whitelist paths for the hg19 and hg38 dbs need only be specified for Exomiser v13.3.0 and earlier (unless specifying your own whitelist), as Exomiser v14.0.0 now includes this in the db.
 
+To save on diskspace we recommend limiting the Exomiser output to JSON, this can be specified by setting the `output_formats` field in the `config.yaml` to [JSON]
+
 If using optional databases, such as REMM/CADD/local frequency the optional data input should look like so in the input
 directory:
 
@@ -142,7 +150,7 @@ The overall structure of the input directory should look like this with the cadd
 ```
 ### Setting up the testdata directory
 
-The Exomiser plugin for PhEval accepts phenopackets and vcf files as an input for running Exomiser. The plugin can be run in `phenotype_only` mode, where only phenopackets are required as an input, however, this *must* be specified in the `config.yaml`.
+The Exomiser plugin for PhEval accepts phenopackets and vcf files as an input for running Exomiser. The plugin can be run in `phenotype_only` mode, where only phenopackets are required as an input, however, this *must* be specified in the `config.yaml` by setting `variant_analysis: False`
 
 The testdata directory should include subdirectories named `phenopackets` and `vcf` if running with variant prioritisation.
 
@@ -182,3 +190,4 @@ To fix the error, `setuptools` needs to be downgraded to version 66:
 pip uninstall setuptools
 pip install -U setuptools=="66"
 ```
+

{pheval_exomiser-0.2.3 → pheval_exomiser-0.2.4}/README.md

@@ -4,7 +4,13 @@ This is the Exomiser plugin for PhEval. With this plugin, you can leverage the v
 
 ## Installation
 
-Clone the pheval.exomiser repo and set up the poetry environment:
+You can install the Exomiser directly with PyPi (recommended):
+
+```shell
+pip install pheval.exomiser
+```
+
+Alternatively you can clone the pheval.exomiser repo and set up the poetry environment:
 
 ```shell
 git clone https://github.com/monarch-initiative/pheval.exomiser.git
@@ -57,6 +63,8 @@ The analysis configuration file (in this case: `preset-exome-analysis.yml`) shou
 
 The whitelist paths for the hg19 and hg38 dbs need only be specified for Exomiser v13.3.0 and earlier (unless specifying your own whitelist), as Exomiser v14.0.0 now includes this in the db.
 
+To save on diskspace we recommend limiting the Exomiser output to JSON, this can be specified by setting the `output_formats` field in the `config.yaml` to [JSON]
+
 If using optional databases, such as REMM/CADD/local frequency the optional data input should look like so in the input
 directory:
 
@@ -119,7 +127,7 @@ The overall structure of the input directory should look like this with the cadd
 ```
 ### Setting up the testdata directory
 
-The Exomiser plugin for PhEval accepts phenopackets and vcf files as an input for running Exomiser. The plugin can be run in `phenotype_only` mode, where only phenopackets are required as an input, however, this *must* be specified in the `config.yaml`.
+The Exomiser plugin for PhEval accepts phenopackets and vcf files as an input for running Exomiser. The plugin can be run in `phenotype_only` mode, where only phenopackets are required as an input, however, this *must* be specified in the `config.yaml` by setting `variant_analysis: False`
 
 The testdata directory should include subdirectories named `phenopackets` and `vcf` if running with variant prioritisation.
 
@@ -158,4 +166,4 @@ To fix the error, `setuptools` needs to be downgraded to version 66:
 ```shell
 pip uninstall setuptools
 pip install -U setuptools=="66"
-```
+```

{pheval_exomiser-0.2.3 → pheval_exomiser-0.2.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pheval_exomiser"
-version = "0.2.3"
+version = "0.2.4"
 description = ""
 authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>",
     "Julius Jacobsen <j.jacobsen@qmul.ac.uk>",
@@ -19,7 +19,7 @@ pyaml = "^21.10.1"
 oaklib = "^0.5.12"
 docker = "^6.0.1"
 pydantic = "^1.10.7"
-pheval = "^0.3.1"
+pheval = "^0.4.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.1.2"