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one based numbering of primer pairs #53

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Sep 27, 2024
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one based numbering of primer pairs #53

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e2a4880
one based numbering of primer pairs
sanjaynagi Sep 27, 2024
a647f31
v2.0.1
sanjaynagi Sep 27, 2024
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7 changes: 5 additions & 2 deletions AnoPrimer/design.py
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Original file line number Diff line number Diff line change
Expand Up @@ -422,7 +422,9 @@ def primer3_to_pandas(primer_dict, assay_type):
# Create a column which is primer pair #, and a column for primer
# parameter which does not contain primer pair #
primer_df = primer_df.iloc[row_start:, :].copy()
primer_df["primer_pair"] = primer_df["parameter"].str.extract("([0-9][0-9]|[0-9])")
primer_df["primer_pair"] = (
primer_df["parameter"].str.extract("([0-9][0-9]|[0-9])").astype(int) + 1
)
primer_df["parameter"] = primer_df["parameter"].str.replace(
"(_[0-9][0-9]|_[0-9])", "", regex=True
)
Expand All @@ -446,7 +448,8 @@ def primer3_to_pandas(primer_dict, assay_type):
required_info = [string.lower() for string in required_info]

# Subset data frame
primer_df = primer_df.loc[required_info, np.arange(primer_df.shape[1]).astype(str)]
primer_df = primer_df.loc[required_info, np.arange(1, primer_df.shape[1] + 1)]
primer_df.columns = primer_df.columns.astype(str)
return primer_df


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2 changes: 1 addition & 1 deletion pyproject.toml
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@@ -1,6 +1,6 @@
[tool.poetry]
name = "AnoPrimer"
version = "2.0.0"
version = "2.0.1"
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/"
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9 changes: 9 additions & 0 deletions tests/run_ci_notebooks.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@

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