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Fixes for one based pairs #54

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merged 3 commits into from
Sep 27, 2024
Merged

Fixes for one based pairs #54

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2b21a8a
fixes for 1 based numbering
sanjaynagi Sep 27, 2024
62170bc
merge
sanjaynagi Sep 27, 2024
4367516
fix
sanjaynagi Sep 27, 2024
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21 changes: 11 additions & 10 deletions AnoPrimer/evaluate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -178,12 +178,12 @@ def plot_primer_snp_frequencies(

# Loop through each primer pair and get the frequencies of alternate alleles
res_dict = {}
for i in range(len(self.df.columns)):
res_dict[i] = _get_primer_alt_frequencies(
for pair in self.df:
res_dict[pair] = _get_primer_alt_frequencies(
species=self.species,
primer_df=self.df,
gdna_pos=self.gdna_pos,
pair=i,
pair=pair,
assay_type=self.assay_type,
contig=self.contig,
sample_sets=sample_sets,
Expand Down Expand Up @@ -354,6 +354,7 @@ def _plot_primers(self, ax, oligos):
handles, labels = ax.get_legend_handles_labels()
for pair in self.df:
pair = int(pair)
pair_idx = pair - 1 # python based indexing
for oligo in oligos:
oligo_pos = _retrieve_span(
primer_df=self.df,
Expand All @@ -367,34 +368,34 @@ def _plot_primers(self, ax, oligos):
if oligo == "forward":
plt.arrow(
lower,
0.8 + (2 / (10 - (pair))),
0.8 + (2 / (10 - (pair_idx))),
upper - lower,
0,
width=0.03,
length_includes_head=True,
color=pal[pair],
color=pal[pair_idx],
)
elif oligo == "reverse":
plt.arrow(
upper,
0.8 + (2 / (10 - (pair))),
0.8 + (2 / (10 - (pair_idx))),
lower - upper,
0,
width=0.03,
length_includes_head=True,
color=pal[pair],
color=pal[pair_idx],
)
elif oligo == "probe":
ax.axhline(y=0.8 + (2 / (10 - (pair))), xmin=lower, xmax=upper)
ax.axhline(y=0.8 + (2 / (10 - (pair_idx))), xmin=lower, xmax=upper)
line = plt.Line2D(
(lower, upper),
(0.8 + (2 / (10 - (pair))), 0.8 + (2 / (10 - (pair)))),
lw=2.5,
color=pal[pair],
color=pal[pair_idx],
)
ax.add_line(line)

patch = patches.Patch(color=pal[pair], label=f"pair {pair}")
patch = patches.Patch(color=pal[pair_idx], label=f"pair {pair}")
handles.append(patch)

return handles
Expand Down
39 changes: 19 additions & 20 deletions AnoPrimer/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -327,30 +327,29 @@ def _plotly_primers(
fig.update_annotations(font_size=13)
for idx, oligo in enumerate(oligos):
idx = idx + 1
for i in primer_df:
i = int(i)
row_i = i + 1
for pair in primer_df:
row_i = int(pair)

color = [
-1 if v == 0 else 1 if v > 0 else 0
for v in res_dict[i][oligo]["alt_frequency"]
for v in res_dict[pair][oligo]["alt_frequency"]
]
colorscale = [[0, "lightgray"], [0.5, "lightgray"], [1, "dodgerblue"]]

tm = np.round(primer_df.loc[f"primer_{oligo}_tm", str(i)], 2)
gc = np.round(primer_df.loc[f"primer_{oligo}_gc_percent", str(i)], 2)
span = f"{int(res_dict[i][oligo]['position'].min())}-{int(res_dict[i][oligo]['position'].max())}"
# Write text to plot for Tm, GC, span, and 3/5'
tm = np.round(primer_df.loc[f"primer_{oligo}_tm", pair], 2)
gc = np.round(primer_df.loc[f"primer_{oligo}_gc_percent", pair], 2)
span = f"{int(res_dict[pair][oligo]['position'].min())}-{int(res_dict[pair][oligo]['position'].max())}"

for col in res_dict[i][oligo].columns:
for col in res_dict[pair][oligo].columns:
if col.endswith("freq"):
res_dict[i][oligo][col] = np.round(res_dict[i][oligo][col], 2)
res_dict[pair][oligo][col] = np.round(res_dict[pair][oligo][col], 2)

fig.add_trace(
go.Scatter(
x=res_dict[i][oligo]["base_pos"],
y=res_dict[i][oligo]["alt_frequency"],
customdata=res_dict[i][oligo][
x=res_dict[pair][oligo]["base_pos"],
y=res_dict[pair][oligo]["alt_frequency"],
customdata=res_dict[pair][oligo][
["A_freq", "C_freq", "G_freq", "T_freq", "base_pos"]
],
hovertemplate=hover_template,
Expand All @@ -369,39 +368,39 @@ def _plotly_primers(
fig.add_annotation(
row=row_i,
col=idx,
x=res_dict[i][oligo]["base_pos"][0],
x=res_dict[pair][oligo]["base_pos"][0],
y=0.8,
text="5'",
showarrow=False,
)
fig.add_annotation(
row=row_i,
col=idx,
x=res_dict[i][oligo]["base_pos"].to_numpy()[-1],
x=res_dict[pair][oligo]["base_pos"].to_numpy()[-1],
y=0.8,
text="3'",
showarrow=False,
)
fig.add_annotation(
row=row_i,
col=idx,
x=res_dict[i][oligo]["base_pos"].to_numpy()[4],
x=res_dict[pair][oligo]["base_pos"].to_numpy()[4],
y=0.92,
text=span,
showarrow=False,
)
fig.add_annotation(
row=row_i,
col=idx,
x=res_dict[i][oligo]["base_pos"].to_numpy()[-7],
x=res_dict[pair][oligo]["base_pos"].to_numpy()[-7],
y=0.92,
text=f"GC={gc}",
showarrow=False,
)
fig.add_annotation(
row=row_i,
col=idx,
x=res_dict[i][oligo]["base_pos"].to_numpy()[-3],
x=res_dict[pair][oligo]["base_pos"].to_numpy()[-3],
y=0.92,
text=f"TM={tm}",
showarrow=False,
Expand All @@ -411,8 +410,8 @@ def _plotly_primers(
row=row_i,
col=idx,
tickmode="array",
tickvals=res_dict[i][oligo]["base_pos"],
ticktext=res_dict[i][oligo]["base"],
tickvals=res_dict[pair][oligo]["base_pos"],
ticktext=res_dict[pair][oligo]["base"],
tickangle=0,
mirror=True,
)
Expand Down Expand Up @@ -446,7 +445,7 @@ def _plotly_primers(

# fig.update_traces(customdata=customdata, hovertemplate=hovertemplate)
fig.update_layout(
height=200 * len(primer_df.columns),
height=220 * len(primer_df.columns),
width=500 * len(oligos),
title_text=title_text,
title_x=0.5,
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 = "AnoPrimer"
version = "2.0.1"
version = "2.0.2"
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/"
Expand Down
16 changes: 8 additions & 8 deletions tests/run_ci_notebooks.sh
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Original file line number Diff line number Diff line change
@@ -1,9 +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
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 &&
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-short.ipynb tests/short_run.ipynb -k AnoPrimer
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