diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a143e93..e4b1a27 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,4 +1,3 @@ -# https://pre-commit.com/ repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.4.0 @@ -6,12 +5,10 @@ repos: - 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 diff --git a/AgamPrimer/AgamPrimer.py b/AgamPrimer/AgamPrimer.py index 9255bab..990940a 100644 --- a/AgamPrimer/AgamPrimer.py +++ b/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) diff --git a/poetry.lock b/poetry.lock index 4611155..b961b61 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2893,14 +2893,14 @@ webpdf = ["pyppeteer (>=1,<1.1)"] [[package]] name = "nbformat" -version = "5.8.0" +version = "5.9.0" description = "The Jupyter Notebook format" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - 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