From 02d7e62ff4a0cb19de5c1ad7a272b6c746d7408e Mon Sep 17 00:00:00 2001 From: Sanjay C Nagi Date: Fri, 11 Oct 2024 10:05:05 +0100 Subject: [PATCH 1/2] fix probe targeting --- AnoPrimer/design.py | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/AnoPrimer/design.py b/AnoPrimer/design.py index d733975..e407043 100644 --- a/AnoPrimer/design.py +++ b/AnoPrimer/design.py @@ -179,14 +179,11 @@ def prepare_gDNA_sequence( } if "probe" in assay_type: - seq_parameters["SEQUENCE_INTERNAL_EXCLUDED_REGION"] = [ - [1, target_loc_primer3[0] - probe_exclude_region_size], - [ - target_loc_primer3[0] + probe_exclude_region_size, - len(target_sequence) - - (target_loc_primer3[0] + probe_exclude_region_size), - ], + seq_parameters["SEQUENCE_INTERNAL_OVERLAP_JUNCTION_LIST"] = [ + target_loc_primer3[0] ] + seq_parameters["PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION"] = 3 + seq_parameters["PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION"] = 3 return seq_parameters From e07ca24dd5ff388fabf3dd641785984a01fd5986 Mon Sep 17 00:00:00 2001 From: Sanjay C Nagi Date: Fri, 11 Oct 2024 10:17:39 +0100 Subject: [PATCH 2/2] removve duplicate exons in plot_primer_locs() --- AnoPrimer/evaluate.py | 3 +++ pyproject.toml | 2 +- tests/run_ci_notebooks.sh | 3 +-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/AnoPrimer/evaluate.py b/AnoPrimer/evaluate.py index b11ed39..2e54c4a 100644 --- a/AnoPrimer/evaluate.py +++ b/AnoPrimer/evaluate.py @@ -270,6 +270,9 @@ def plot_primer_locs( print("No exons in close proximity for loc plot") return + # remove duplicate exons from different transcripts + locgff = locgff.drop_duplicates("Name") + # Set up the plot fig, ax = plt.subplots(1, 1, figsize=[16, 4]) self._configure_plot_axes(ax, min_, max_, start, end) diff --git a/pyproject.toml b/pyproject.toml index c532e56..b1aa7d6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "AnoPrimer" -version = "2.0.4" +version = "2.0.5" 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/" diff --git a/tests/run_ci_notebooks.sh b/tests/run_ci_notebooks.sh index 15cc2b0..938d3d8 100755 --- a/tests/run_ci_notebooks.sh +++ b/tests/run_ci_notebooks.sh @@ -1,8 +1,7 @@ - +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.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 &&