Merge pull request #37 from sanjaynagi/fix-bug-06-07-23

fix bug in designPrimers()

AgamPrimer/AgamPrimer.py

@@ -734,7 +734,7 @@ def designPrimers(
 
     if assay_type != "probe":
         # check if primer3 has returned any primers
-        if int(primer_dict["PRIMER_PAIR_EXPLAIN"][-1]) == 0:
+        if int(extract_trailing_digits(primer_dict["PRIMER_PAIR_EXPLAIN"])):
             print(
                 f"No primers found for {assay_name}. For cDNA primers, this is more likely to occur if the target contains only one exon-exon junction. see troubleshooting below for more information. We suggest relaxing the primer parameters \n"
             )
@@ -796,6 +796,16 @@ def designPrimers(
     return (primer_df, blat_df)
 
 
+def extract_trailing_digits(string):
+    import re
+
+    match = re.search(r"\d+$", string)
+    if match:
+        return match.group(0)
+    else:
+        return None
+
+
 def _get_primer_arrays(contig, gdna_pos, sample_sets, assay_type, sample_query=None):
     if any(item in assay_type for item in ["gDNA", "probe"]):
         span_str = f"{contig}:{gdna_pos.min()}-{gdna_pos.max()}"

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "AgamPrimer"
-version = "0.6.3"
+version = "0.6.4"
 description = "A package to design primers in Anopheles gambiae whilst considering genetic variation with malariagen_data"
 authors = [
     "Sanjay Nagi <sanjay.nagi@lstmed.ac.uk>",