From b064e536ec78448d509dc6f9125a56e5565555b6 Mon Sep 17 00:00:00 2001
From: Sanjay C Nagi <sanjay.c.nagi@gmail.com>
Date: Fri, 27 Sep 2024 16:06:51 +0100
Subject: [PATCH] fixes

---
 AnoPrimer/evaluate.py     | 30 ++++++++++++++++++++++++++++--
 AnoPrimer/utils.py        | 26 +-------------------------
 tests/run_ci_notebooks.sh |  6 +++---
 3 files changed, 32 insertions(+), 30 deletions(-)

diff --git a/AnoPrimer/evaluate.py b/AnoPrimer/evaluate.py
index 547d34c..3e8a0e1 100644
--- a/AnoPrimer/evaluate.py
+++ b/AnoPrimer/evaluate.py
@@ -12,7 +12,6 @@
     _plotly_primers,
     _retrieve_span,
     _return_oligo_list,
-    add_spans_to_df,
     retrieve_data_resource,
     round_floats_in_df,
 )
@@ -73,7 +72,6 @@ def __init__(
         self.assay_type = assay_type
         self.assay_name = assay_name
 
-        self.df = round_floats_in_df(add_spans_to_df(primer_df), decimal_places=2)
         self.seq_parameters = seq_parameters
         self.primer_parameters = primer_parameters
 
@@ -81,6 +79,9 @@ def __init__(
         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,
@@ -122,6 +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.
diff --git a/AnoPrimer/utils.py b/AnoPrimer/utils.py
index a2ef0cd..6b58c48 100644
--- a/AnoPrimer/utils.py
+++ b/AnoPrimer/utils.py
@@ -153,30 +153,6 @@ def _plotly_frequencies(
 
 
 #### utility functions ####
-def add_spans_to_df(primers):
-    df = primers.df
-    oligos, _ = _return_oligo_list(assay_type=primers.assay_type)
-
-    oligo_spans = {}
-    for oligo in oligos:
-        spans = []
-        for pair in df:
-            pos = _retrieve_span(
-                df,
-                gdna_pos=primers.gdna_pos,
-                oligo=oligo,
-                assay_type=primers.assay_type,
-                pair=pair,
-            )
-            span = f"{primers.contig}:{pos.min()}-{pos.max()}"
-            spans.append(span)
-
-        oligo_spans[oligo] = pd.Series(
-            spans, name=f"primer_{oligo}_span", index=primers.df.columns
-        )
-        df = pd.concat([df, oligo_spans[oligo].to_frame().T])
-
-    return df
 
 
 def round_floats_in_df(df, decimal_places=1):
@@ -193,7 +169,7 @@ def round_if_float(val):
         except (ValueError, TypeError):
             return val
 
-    return df.map(round_if_float)
+    return df.applymap(round_if_float)
 
 
 def extract_trailing_digits(string):
diff --git a/tests/run_ci_notebooks.sh b/tests/run_ci_notebooks.sh
index b72f6e3..15cc2b0 100755
--- a/tests/run_ci_notebooks.sh
+++ b/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