Merge pull request #53 from sanjaynagi/1-based-numbering-27-09-24

one based numbering of primer pairs

AnoPrimer/design.py

@@ -422,7 +422,9 @@ def primer3_to_pandas(primer_dict, assay_type):
     # Create a column which is primer pair #, and a column for primer
     # parameter which does not contain primer pair #
     primer_df = primer_df.iloc[row_start:, :].copy()
-    primer_df["primer_pair"] = primer_df["parameter"].str.extract("([0-9][0-9]|[0-9])")
+    primer_df["primer_pair"] = (
+        primer_df["parameter"].str.extract("([0-9][0-9]|[0-9])").astype(int) + 1
+    )
     primer_df["parameter"] = primer_df["parameter"].str.replace(
         "(_[0-9][0-9]|_[0-9])", "", regex=True
     )
@@ -446,7 +448,8 @@ def primer3_to_pandas(primer_dict, assay_type):
     required_info = [string.lower() for string in required_info]
 
     # Subset data frame
-    primer_df = primer_df.loc[required_info, np.arange(primer_df.shape[1]).astype(str)]
+    primer_df = primer_df.loc[required_info, np.arange(1, primer_df.shape[1] + 1)]
+    primer_df.columns = primer_df.columns.astype(str)
     return primer_df
 
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "AnoPrimer"
-version = "2.0.0"
+version = "2.0.1"
 description = "A package to design primers in Anopheles gambiae whilst considering genetic variation with malariagen_data"
 readme = "README.md"
 documentation = "https://sanjaynagi.github.io/anoprimer/latest/"

tests/run_ci_notebooks.sh

@@ -0,0 +1,9 @@
+
+papermill notebooks/AnoPrimer-long.ipynb qPCR_run.ipynb -k AnoPrimer -f tests/cDNA_Params_fun.json &&
+papermill notebooks/AnoPrimer-long.ipynb qPCR2_run.ipynb -k AnoPrimer -f tests/cDNA_Params_2_fun.json &&
+papermill notebooks/AnoPrimer-long.ipynb gDNA_run.ipynb -k AnoPrimer -f tests/gDNA_probe_Params_fun.json &&
+papermill notebooks/AnoPrimer-long.ipynb qPCR_run.ipynb -k AnoPrimer -f tests/cDNA_Params.json &&
+papermill notebooks/AnoPrimer-long.ipynb qPCR2_run.ipynb -k AnoPrimer -f tests/cDNA_Params_2.json &&
+papermill notebooks/AnoPrimer-long.ipynb gDNA_run.ipynb -k AnoPrimer -f tests/gDNA_probe_Params.json &&
+papermill notebooks/AnoPrimer-long.ipynb probe_run.ipynb -k AnoPrimer -f tests/probe_Params.json &&
+papermill notebooks/AnoPrimer-short.ipynb short_run.ipynb -k AnoPrimer