add sample plan

feldman4 · Feb 5, 2024 · 5062a54 · 5062a54
1 parent b28e7e2
commit 5062a54
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Showing 3 changed files with 10 additions and 0 deletions.
diff --git a/.gitignore b/.gitignore
@@ -4,6 +4,7 @@ examples/paired_reads/*
 !examples/paired_reads/config.yaml
 !examples/paired_reads/reference_dna.csv
 !examples/paired_reads/samples.csv
+!examples/paired_reads/sample_plan.csv
 !examples/paired_reads/planned_dna.csv
 !examples/paired_reads/pattern*.png
 !examples/paired_reads/paired_read_example.ipynb

diff --git a/examples/paired_reads/sample_plan.csv b/examples/paired_reads/sample_plan.csv
@@ -0,0 +1,6 @@
+sample,source,coverage
+sample_A,pool1,50
+sample_B,pool2,50
+sample_C,pool1,50
+sample_C,pool2,20
+sample_D,pool3,50
diff --git a/src/ngs_analysis/app.py b/src/ngs_analysis/app.py
@@ -75,6 +75,9 @@ def dna_to_designs():
     """
     df_reference = load_reference_dna()
     config = load_config()
+    config['left_adapter'] = config.get('left_adapter_reference', config['left_adapter'])
+    config['right_adapter'] = config.get('right_adapter_reference', config['right_adapter'])
+
     parsed = (parse_sequences(config, df_reference['reference_dna'])
      .drop('read_index', axis=1))
     m, n = len(parsed), len(df_reference)