merge

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
 
 

AnoPrimer/evaluate.py

@@ -248,9 +248,10 @@ def plot_primer_locs(
         # Plot exons, genes, primer spans
         self._plot_exons(ax, locgff, exon_id_col)
         self._plot_genes(ax, genegff, min_, max_)
-        self._plot_primers(ax, oligos)
+        handles = self._plot_primers(ax, oligos)
+
         # Add legend and save if out_dir is provided
-        plt.legend(handles=ax.get_legend_handles_labels()[0], loc=legend_loc)
+        plt.legend(handles=handles, loc=legend_loc)
         if out_dir:
             fig.savefig(
                 f"{out_dir}/{assay_name}_primer_locs.png", dpi=300, bbox_inches="tight"
@@ -397,6 +398,8 @@ def _plot_primers(self, ax, oligos):
             patch = patches.Patch(color=pal[pair], label=f"pair {pair}")
             handles.append(patch)
 
+        return handles
+
     def gget_blat_genome(self, assembly="anoGam3"):
         """
         Align primers to the genome using BLAT.