Merge pull request #32 from sanjaynagi/support-for-primer3py-2-01-06-23

Support for and pin primer3-py v2.0.0

.pre-commit-config.yaml

@@ -1,17 +1,14 @@
-# https://pre-commit.com/
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
-  # isort should run before black as black sometimes tweaks the isort output
   - repo: https://github.com/pycqa/isort
     rev: 5.12.0
     hooks:
       - id: isort
-  # https://github.com/python/black#version-control-integration
   - repo: https://github.com/psf/black
     rev: 23.1.0
     hooks:
@@ -20,7 +17,7 @@ repos:
     rev: v0.3.8
     hooks:
       - id: blackdoc
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
+  # - repo: https://github.com/pycqa/flake8
+  #   rev: 6.0.0
+  #   hooks:
+  #     - id: flake8

AgamPrimer/AgamPrimer.py

@@ -137,7 +137,6 @@ def primer_params(
     amplicon_size_range=None,
     generate_defaults=False,
 ):
-
     """
     adds necessary parameters depending on assay_type, or can
     generate the default parameters
@@ -646,7 +645,6 @@ def designPrimers(
 
 
 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()}"
         snps = ag3.snp_calls(
@@ -744,7 +742,6 @@ def _plotly_primers(
     target,
     out_dir=None,
 ):
-
     oligos, _ = _return_oligo_list(assay_type)
     if len(oligos) == 2:
         plt_title = ["Forward primer", "Reverse primer"]
@@ -933,13 +930,13 @@ def _get_qPCR_locs(gff, contig, transcript):
 def _return_oligo_list(assay_type):
     if assay_type == "probe":
         oligos = ["probe"]
-        row_start = 5
+        row_start = 9
     elif any(item == assay_type for item in ["gDNA primers", "cDNA primers"]):
         oligos = ["forward", "reverse"]
-        row_start = 7
+        row_start = 11
     elif assay_type == "gDNA primers + probe":
         oligos = ["forward", "reverse", "probe"]
-        row_start = 8
+        row_start = 12
     return (oligos, row_start)
 
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "AgamPrimer"
-version = "0.6.0"
+version = "0.6.1"
 description = "A package to design primers in Anopheles gambiae whilst considering genetic variation with malariagen_data"
 authors = [
     "Sanjay Nagi <[email protected]>",
@@ -12,7 +12,7 @@ license = "MIT"
 
 [tool.poetry.dependencies]
 python = ">=3.8,<3.12"
-primer3-py = "*"
+primer3-py = "2.0.0"
 malariagen_data = "*"
 openpyxl = "*"
 gget = "*"