Merge branch 'main' into refactor

belowlab · Nov 27, 2023 · f6c3d6c · f6c3d6c
2 parents cff903b + e212f57
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diff --git a/README.md b/README.md
@@ -4,14 +4,15 @@
 
 # DRIVE:
 
-This repository contains the source code for the tool DRIVE v1.0.0. Distant Relatedness for Identification and Variant Evaluation (DRIVE) is a novel approach to IBD-based genotype inference used to identify shared chromosomal segments in dense genetic arrays. DRIVE implemented a random walk algorithm that identifies clusters of individuals who pairwise share an IBD segment overlapping a locus of interest. This tool was developed in python by the Below Lab at Vanderbilt University. The documentation for how to use this tool can be found here [DRIVE documentation](https://drive-ibd.readthedocs.io/en/latest/)
+This repository contains the source code for the tool DRIVE (Distant Relatedness for Identification and Variant Evaluation) is a novel approach to IBD-based genotype inference used to identify shared chromosomal segments in dense genetic arrays. DRIVE implements a random walk algorithm that identifies clusters of individuals who pairwise share an IBD segment overlapping a locus of interest. This tool was developed in python by the Below Lab at Vanderbilt University. The documentation for how to use this tool can be found here [DRIVE documentation](https://drive-ibd.readthedocs.io/en/latest/)
 
 ## Installing DRIVE:
 DRIVE is available on PYPI and can easily be installed using the following command:
 
 ```bash
 pip install drive-ibd
 ```
+It is recommended to install DRIVE within a virtual environment such as venv, or conda. More information about this process can be found within the documentation.
 
 If the user wishes to develop DRIVE or install the program from source then they can clone the repository. This process is described under the section called "Github Installation" in the documentation.
 

diff --git a/drive/utilities/parser/case_file_parser.py b/drive/utilities/parser/case_file_parser.py
@@ -154,7 +154,7 @@ def _determine_status(
                 logger.warning(
                     f"The status for individual, {grid_id}, was not recognized. The status found in the file was {value} for phenotype {phenotype_mapping}. This individual will be added to the exclusion list but it is recommended that the user checks to ensure that this is not a typo in the phenotype file."  # noqa: E501
                 )
-                phenotype_dict[phenotype_mapping]["excluded"].append(grid_id)
+                phenotype_dict[phenotype_mapping]["excluded"].add(grid_id)
 
     def _create_phenotype_dictionary(
         self,

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,5 +1,6 @@
 [tool.poetry]
 name = "drive-ibd"
+
 version = "2.2.0"
 description = "cli tool to identify networks of individuals who share IBD segments overlapping loci of interest"
 authors = ["James Baker <[email protected]>", "Hung-Hsin Chen <[email protected]>", "Jennifer E. Below <[email protected]>"]