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eastgenomics · Dec 20, 2024 · 4a2f3b3 · 4a2f3b3
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diff --git a/DI-1299/README.md b/DI-1299/README.md
@@ -1,9 +1,9 @@
 # Compare Somalier outputs in GRCh37 and GRCh38
 
-### Description
+## Description
 The `compare_b37_and_b38.py` script is used to compare Somalier Predicted_Sex values for samples in GRCh37 and GRCh38 and return any mismatches.
 
-### Inputs
+## Inputs
 - `--config (str)`: Path to a config file with relevant variables for the assay.
 
 Example config:
@@ -33,21 +33,21 @@ Example config:
 }
 ```
 
-### Running
+## Running
 Example command:
-```
+```bash
 python compare_b37_and_b38.py --config TWE_config.json
 ```
 
-### How it works
+## How it works
 The script:
 - Find all projects using the `search_term` in GRCh38 in DNAnexus.
 - Gets the related GRCh37 project for each GRCh38 project with the prefix `002_` and the suffix `_{assay}`.
- - Within the GRCh37 and GRCh38 projects, find all files by `filename` and reads them all in with pandas.
+  - Within the GRCh37 and GRCh38 projects, find all files by `filename` and reads them all in with pandas.
 - Identifies any mismatches in `column_to_compare` between the GRCh37 and GRCh38 values for each sample and investigate.
 - If mismatches are found, plots the variables in `variables_to_plot` to look at differences in these values for each sample between genome builds.
 
-### Output
+## Output
 - `{assay}_all_results.tsv`: A TSV with Somalier results for all samples found; headers have '_GRCh37' and '_GRCh38' suffixes to show which genome the result is from.
 - `{assay}_all_mismatches.tsv`: A TSV with all rows where there is a mismatch between the `column_to_compare` value in GRCh37 and GRCh38.
 - If there are samples with mismatches found, one plot is created for all metrics included in each nested list within `variables_to_plot` for each sample in GRCh37 and GRCh38. Each variable in each nested list is plotted as a scatter plot, one per row, and each plot is saved to HTML.
diff --git a/DI-1299/compare_b37_and_b38.py b/DI-1299/compare_b37_and_b38.py
@@ -89,25 +89,7 @@ def get_config_info(config_dict):
         "variables_to_plot",
     ]
 
-    (
-        assay,
-        search_term,
-        number_of_projects,
-        filename,
-        column_to_compare,
-        sample_column,
-        variables_to_plot,
-    ) = list(map(config_dict.get, keys))
-
-    return (
-        assay,
-        search_term,
-        number_of_projects,
-        filename,
-        column_to_compare,
-        sample_column,
-        variables_to_plot,
-    )
+    return list(map(config_dict.get, keys))
 
 
 def find_projects(search_term, number_of_projects=None):

diff --git a/README.md b/README.md
@@ -3,14 +3,14 @@ Repository for code related to small tasks for supporting the RD service.
 
 |  Ticket   |   Summary   |
 |   ---     |     ---     |
-| [EBH-3050] | Determine how many workbooks were released/not released (based on number of variants filtered) per clinical indication since new filtering introduced
-| [DI-773] | Gather and plot QC metrics
-| [DI-1057] | Validate East GLH RD Test Directory hosted on AWS RDS
-| [DI-1094] | CEN/WES GRCh38 egg_sex_check thresholds - August 2024
-| [DI-1189] | Create new PanelApp JSON file
-| [DI-435] | Find and merge VCFs for creation of a GRCh38 POP AF VCF
-| [DI-1294] | Remove any content from the PID fields in workbooks in a given path
-| [DI-1299] | Compare values between GRCh37 and GRCh38 for Somalier
+| [EBH-3050] | Determine how many workbooks were released/not released (based on number of variants filtered) per clinical indication since new filtering introduced |
+| [DI-773] | Gather and plot QC metrics |
+| [DI-1057] | Validate East GLH RD Test Directory hosted on AWS RDS |
+| [DI-1094] | CEN/WES GRCh38 egg_sex_check thresholds - August 2024 |
+| [DI-1189] | Create new PanelApp JSON file |
+| [DI-435] | Find and merge VCFs for creation of a GRCh38 POP AF VCF |
+| [DI-1294] | Remove any content from the PID fields in workbooks in a given path |
+| [DI-1299] | Compare values between GRCh37 and GRCh38 for Somalier |
 
 
 [EBH-3050]: https://cuhbioinformatics.atlassian.net/browse/EBH-3050
@@ -19,5 +19,5 @@ Repository for code related to small tasks for supporting the RD service.
 [DI-1094]: https://cuhbioinformatics.atlassian.net/browse/DI-1094
 [DI-1189]: https://cuhbioinformatics.atlassian.net/browse/DI-1189
 [DI-435]: https://cuhbioinformatics.atlassian.net/browse/DI-435
-[DI-1294]: https://cuhbioinformatics.atlassian.net/issues/DI-1294
-[DI-1299]: https://cuhbioinformatics.atlassian.net/browse/DI-1299
+[DI-1294]: https://cuhbioinformatics.atlassian.net/browse/DI-1294
+[DI-1299]: https://cuhbioinformatics.atlassian.net/browse/DI-1299