Merge pull request #55 from sanjaynagi/addspanstodf

Add primer spans to dataframe and round floats

AnoPrimer/evaluate.py

@@ -13,6 +13,7 @@
     _retrieve_span,
     _return_oligo_list,
     retrieve_data_resource,
+    round_floats_in_df,
 )
 
 
@@ -71,14 +72,16 @@ def __init__(
         self.assay_type = assay_type
         self.assay_name = assay_name
 
-        self.df = primer_df
         self.seq_parameters = seq_parameters
         self.primer_parameters = primer_parameters
 
         # Extract additional attributes from seq_parameters
         self.target_sequence = seq_parameters.get("SEQUENCE_TEMPLATE")
         self.gdna_pos = np.array(seq_parameters.get("GENOMIC_DNA_POSITIONS"))
 
+        self.df = primer_df
+        self.df = round_floats_in_df(self.add_spans_to_df(), decimal_places=2)
+
     def evaluate_primers(
         self,
         sample_sets,
@@ -120,6 +123,31 @@ def evaluate_primers(
             if out_dir is not None and blat_df is not None:
                 blat_df.to_csv(f"{out_dir}/{self.assay_name}_blat_results.csv")
 
+    def add_spans_to_df(self):
+        df = self.df
+        oligos, _ = _return_oligo_list(assay_type=self.assay_type)
+
+        oligo_spans = {}
+        for oligo in oligos:
+            spans = []
+            for pair in df:
+                pos = _retrieve_span(
+                    df,
+                    gdna_pos=self.gdna_pos,
+                    oligo=oligo,
+                    assay_type=self.assay_type,
+                    pair=pair,
+                )
+                span = f"{self.contig}:{pos.min()}-{pos.max()}"
+                spans.append(span)
+
+            oligo_spans[oligo] = pd.Series(
+                spans, name=f"primer_{oligo}_span", index=self.df.columns
+            )
+            df = pd.concat([df, oligo_spans[oligo].to_frame().T])
+
+        return df
+
     def summarise_metadata(self, sample_sets=None, sample_query=None):
         """
         Retrieve a summary of metadata for samples in the ag3/af1 resource.
@@ -350,11 +378,20 @@ def _plot_genes(self, ax, genegff, min_, max_):
 
     def _plot_primers(self, ax, oligos):
         """Helper method to plot primers."""
+
+        def _generate_primer_pair_positions(num_pairs, start=1, end=1.45):
+            if num_pairs == 1:
+                return [start]
+
+            step = (end - start) / (num_pairs - 1)
+            return [start + i * step for i in range(num_pairs)]
+
         pal = sns.color_palette("Set2", len(self.df.columns))
         handles, labels = ax.get_legend_handles_labels()
         for pair in self.df:
             pair = int(pair)
             pair_idx = pair - 1  # python based indexing
+            pair_ypos = _generate_primer_pair_positions(len(self.df.columns))
             for oligo in oligos:
                 oligo_pos = _retrieve_span(
                     primer_df=self.df,
@@ -368,7 +405,7 @@ def _plot_primers(self, ax, oligos):
                 if oligo == "forward":
                     plt.arrow(
                         lower,
-                        0.8 + (2 / (10 - (pair_idx))),
+                        pair_ypos[pair_idx],
                         upper - lower,
                         0,
                         width=0.03,
@@ -378,18 +415,19 @@ def _plot_primers(self, ax, oligos):
                 elif oligo == "reverse":
                     plt.arrow(
                         upper,
-                        0.8 + (2 / (10 - (pair_idx))),
+                        pair_ypos[pair_idx],
                         lower - upper,
                         0,
                         width=0.03,
                         length_includes_head=True,
                         color=pal[pair_idx],
                     )
                 elif oligo == "probe":
-                    ax.axhline(y=0.8 + (2 / (10 - (pair_idx))), xmin=lower, xmax=upper)
+                    ax.axhline(y=pair_ypos[pair_idx], xmin=lower, xmax=upper)
                     line = plt.Line2D(
                         (lower, upper),
-                        (0.8 + (2 / (10 - (pair))), 0.8 + (2 / (10 - (pair)))),
+                        pair_ypos[pair_idx],
+                        pair_ypos[pair_idx],
                         lw=2.5,
                         color=pal[pair_idx],
                     )

AnoPrimer/utils.py

@@ -155,6 +155,23 @@ def _plotly_frequencies(
 #### utility functions ####
 
 
+def round_floats_in_df(df, decimal_places=1):
+    import numpy as np
+
+    def round_if_float(val):
+        if isinstance(val, (int, np.integer)):
+            return val
+        try:
+            float_val = float(val)
+            if float_val.is_integer():
+                return int(float_val)
+            return round(float_val, decimal_places)
+        except (ValueError, TypeError):
+            return val
+
+    return df.applymap(round_if_float)
+
+
 def extract_trailing_digits(string):
     import re
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "AnoPrimer"
-version = "2.0.2"
+version = "2.0.3"
 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

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