Merge pull request #14 from jluebeck/master

bugfix for gene_subset_file var name provided by .yaml
AmpliconSuite · Jun 7, 2023 · 2151b0a · 2151b0a
2 parents a2b2d37 + b88290c
commit 2151b0a
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 *BPG_converted_cycles*
 *.pyc
 test_files/
+test.txt
 *.cmap
 *_graph.txt
 *_key.txt

diff --git a/VizUtil.py b/VizUtil.py
@@ -1256,7 +1256,7 @@ def parse_main_args_yaml(args):
         if "seg_label_fontsize" in sample_data:
             args.seg_label_fontsize = sample_data.get("seg_label_fontsize")
         if "gene_subset_file" in sample_data:
-            args.gene_subset_files = sample_data.get("gene_subset_file")
+            args.gene_subset_file = sample_data.get("gene_subset_file")
         if "gene_subset_list" in sample_data:
             args.gene_subset_list = sample_data.get("gene_subset_list")
             print(args.gene_subset_list)

diff --git a/examples/README.md b/examples/README.md
@@ -28,4 +28,5 @@ Data derived from oropharyngeal squamous cell carinoma with hybrid human-viral e
 3. Call CycleViz
 
 **Note that the order in which the feature YAML files are provided specifies the order in which the interior tracks appear (first is innermost, last is outermost).**
->`$CV_SRC/CycleViz.py --input_yaml_file t41_CV.yaml --feature_yaml_list T41_link_track.yaml T41_wgs_track.yaml T41_rna_track.yaml`
+>`$CV_SRC/CycleViz.py --input_yaml_file t41_CV.yaml --feature_yaml_list T41_link_track.yaml T41_wgs_track.yaml T41_rna_track.yaml`
+