def validation_analysis(self, data, clones_observations):
validations = clones_observations.validate_all_clones(
min_band_cutoff=data.bandsRange[0],
max_band_cutoff=data.bandsRange[1],
relative_tolerance=data.tolerance,
)
first_validation = list(validations.values())[0]
ladder = list(first_validation.clone.digestions.values())[0].ladder
# CREATE A ZIP WITH VALIDATION REPORTS
zip_root = flametree.file_tree("@memory")
self.logger(message="Generating the validation report...")
zip_root._file("validations.pdf").write(
clones_observations.plot_all_validations_patterns(validations))
clones_observations.validations_summary_table(
validations,
zip_root._file("summary.csv").open("w"))
if data.includeDigestionPlots:
self.logger(message="Plotting cuts maps...")
co = clones_observations
plot_records_digestions(
target=zip_root._file("digestions.pdf").open("wb"),
ladder=ladder,
records_and_digestions=[
(co.constructs_records[cst], digestion_)
for cst, digestions in co.constructs_digestions.items()
for digestion_ in digestions
],
)
# zip_root._file('digestions.pdf').write(pdf_data)
self.logger(message="Generating the success plate map...")
ax = clones_observations.plot_validations_plate_map(validations)
ax.figure.savefig(
zip_root._file("success_map.pdf").open("wb"),
format="pdf",
bbox_inches="tight",
)
self.logger(message="All done !")
return {
"zip_file": {
"data": data_to_html_data(zip_root._close(), "zip"),
"name": "validation_report.zip",
"mimetype": "application/zip",
},
"success": "yeah!",
}
def validation_analysis(self, data, clones_observations):
validations = clones_observations.validate_all_clones(
min_band_cutoff=data.bandsRange[0],
max_band_cutoff=data.bandsRange[1],
relative_tolerance=data.tolerance)
first_validation = list(validations.values())[0]
ladder = list(first_validation.clone.digestions.values())[0].ladder
# CREATE A ZIP WITH VALIDATION REPORTS
zip_root = flametree.file_tree('@memory')
self.logger(message="Generating the validation report...")
zip_root._file('validations.pdf').write(
clones_observations.plot_all_validations_patterns(validations))
clones_observations.validations_summary_table(
validations,
zip_root._file('summary.csv').open('w'))
if data.includeDigestionPlots:
self.logger(message="Plotting cuts maps...")
co = clones_observations
plot_records_digestions(
target=zip_root._file('digestions.pdf').open('wb'),
ladder=ladder,
records_and_digestions=[
(co.constructs_records[cst], digestion_)
for cst, digestions in co.constructs_digestions.items()
for digestion_ in digestions
])
# zip_root._file('digestions.pdf').write(pdf_data)
self.logger(message="Generating the success plate map...")
ax = clones_observations.plot_validations_plate_map(validations)
ax.figure.savefig(zip_root._file('success_map.pdf').open('wb'),
format='pdf',
bbox_inches='tight')
self.logger(message="All done !")
return {
'zip_file': {
'data': data_to_html_data(zip_root._close(), 'zip'),
'name': 'validation_report.zip',
'mimetype': 'application/zip'
},
'success': 'yeah!'
}
def test_plot_records_digestions_ziplist(tmpdir):
target = os.path.join(str(tmpdir), "test.pdf")
plot_records_digestions(records_and_digestions=list(
zip(records, digestions)),
ladder=LADDER_100_to_4k,
target=target)
def test_plot_records_digestions(tmpdir):
target = os.path.join(str(tmpdir), "test.pdf")
plot_records_digestions(records=records,
digestions=digestions,
ladder=LADDER_100_to_4k,
target=target)
from bandwagon import (
plot_all_digestion_patterns,
plot_records_digestions,
load_record,
LADDER_100_to_4k,
)
import os
records = [
load_record(
os.path.join("records", filename), id=filename, topology="circular"
)
for filename in sorted(os.listdir("records"))
]
digestions = [("BamHI", "NcoI"), ("BsaI", "XbaI"), ("StyI",)]
plot_records_digestions(
records=records,
digestions=digestions,
ladder=LADDER_100_to_4k,
target="plot_records_digestions_example.pdf",
)
axes = plot_all_digestion_patterns(
records=records, digestions=digestions, ladder=LADDER_100_to_4k
)
axes[0].figure.savefig("plot_all_digestion_patterns.png", bbox_inches="tight")
def work(self):
self.logger(message="Exploring possible digestions...")
data = self.data
ladder = LADDERS[data.ladder]
enzymes = data.possible_enzymes
records = records_from_data_files(data.files)
for record in records:
set_record_topology(record, data.topology)
# sequences = OrderedDict(
# [(record.id, str(record.seq)) for record in records]
# )
self.logger(message="Initializing...")
if data.goal == "ideal":
mini, maxi = data.bands_range
problem = IdealDigestionsProblem(
sequences=records,
enzymes=enzymes,
ladder=ladder,
min_bands=mini,
max_bands=maxi,
max_enzymes_per_digestion=data.max_enzymes)
else:
problem = SeparatingDigestionsProblem(
sequences=records,
enzymes=enzymes,
ladder=ladder,
max_enzymes_per_digestion=data.max_enzymes,
)
self.logger(message="Selecting digestions...")
score, selected_digestions = problem.select_digestions(
max_digestions=data.max_digestions, search="full")
bands_props = (None if not data.show_bands_sizes else dict(
label="=size", label_fontdict=dict(size=6)))
axes = problem.plot_digestions(
selected_digestions,
patterns_props={"label_fontdict": {
"rotation": 35
}},
bands_props=bands_props,
)
figure_data = matplotlib_figure_to_svg_base64_data(axes[0].figure,
bbox_inches="tight")
if data.plot_cuts:
ladder = bandwagon.custom_ladder(None, ladder.bands)
self.logger(message="Plotting cuts maps...")
zip_root = flametree.file_tree("@memory")
bandwagon.plot_records_digestions(
target=zip_root._file("Details.pdf").open("wb"),
ladder=ladder,
records_and_digestions=[(rec, digestion) for rec in records
for digestion in selected_digestions],
)
pdf_data = zip_root["Details.pdf"].read("rb")
pdf_data = data_to_html_data(pdf_data, datatype="pdf")
else:
pdf_data = None
return {
"figure_data": figure_data,
"digestions": selected_digestions,
"score": score,
"pdf_data": pdf_data,
}