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add genomic span #34

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merged 2 commits into from
Jul 2, 2023
Merged

add genomic span #34

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7426137
add span
sanjaynagi Jul 2, 2023
067dbd9
fix drop row
sanjaynagi Jul 2, 2023
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33 changes: 27 additions & 6 deletions AgamPrimer/AgamPrimer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -562,6 +562,7 @@ def designPrimers(
"""

# check target is valid for assay type and find contig
oligos, _ = _return_oligo_list(assay_type)
contig, target = check_and_split_target(target=target, assay_type=assay_type)
amplicon_size_range = [[min_amplicon_size, max_amplicon_size]]

Expand Down Expand Up @@ -612,11 +613,6 @@ def designPrimers(
# AgamPrimer.primer3_run_statistics(primer_dict, assay_type)
primer_df = primer3_to_pandas(primer_dict=primer_dict, assay_type=assay_type)

# write primer3 output to file
if out_dir:
primer_df.to_csv(f"{out_dir}/{assay_name}.{assay_type}.tsv", sep="\t")
primer_df.to_excel(f"{out_dir}/{assay_name}.{assay_type}.xlsx")

# plot frequencies of alleles in primer pairs
results_dict = plot_primer_ag3_frequencies(
primer_df=primer_df,
Expand All @@ -628,6 +624,7 @@ def designPrimers(
seq_parameters=seq_parameters,
out_dir=out_dir,
)

# plot primer locations on genome
plot_primer_locs(
primer_res_dict=results_dict,
Expand All @@ -638,9 +635,33 @@ def designPrimers(
legend_loc="lower left",
out_dir=out_dir,
)

# add genomic span to primer_df
spans = []
for oligo in oligos:
for i in range(len(primer_df.columns)):
start = int(results_dict[i][oligo]["position"].min())
end = int(results_dict[i][oligo]["position"].max())
span = f"{start}-{end}"
spans.append(span)

spans = np.array(spans).reshape(len(oligos), len(primer_df.columns))
spans_df = pd.DataFrame(spans)
spans_df.index = [f"{o}_genomic_span" for o in oligos]
spans_df.columns = primer_df.columns
primer_df = pd.concat([primer_df, spans_df], axis=0).drop(
index=[f"primer_{o}" for o in oligos]
)

# check primers for specificity against the genome and write to file
blat_df = gget_blat_genome(primer_df, assay_type, assembly="anoGam3")
blat_df.to_csv(f"{out_dir}/{assay_name}.{assay_type}.blat.tsv", sep="\t")

# write primer3 and blat output to file
if out_dir:
primer_df.to_csv(f"{out_dir}/{assay_name}.{assay_type}.tsv", sep="\t")
primer_df.to_excel(f"{out_dir}/{assay_name}.{assay_type}.xlsx")
blat_df.to_csv(f"{out_dir}/{assay_name}.{assay_type}.blat.tsv", sep="\t")

return (primer_df, blat_df)


Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[tool.poetry]
name = "AgamPrimer"
version = "0.6.1"
version = "0.6.2"
description = "A package to design primers in Anopheles gambiae whilst considering genetic variation with malariagen_data"
authors = [
"Sanjay Nagi <sanjay.nagi@lstmed.ac.uk>",
Expand Down