import pandas
from flametree import file_tree
from ...biotools import write_record
from ...AssemblyMix import AssemblyMixError
from .AssemblyReportPlotsMixin import AssemblyReportPlotsMixin
[docs]class AssemblyReportWriter(AssemblyReportPlotsMixin):
"""Class to configure assembly simulation report writing.
Responsible for writing the final sequence(s) of the assembly in Genbank
format as well as a .csv report on all assemblies produced and PDF figures
to allow a quick overview or diagnostic.
Folder ``assemblies`` contains the final assemblies, ``assembly_graph``
contains a schematic view of how the parts assemble together, folder
``fragments`` contains the details of all fragments produced by the enzyme
digestion, and folder ``provided_parts`` contains the original input
(genbanks of all parts provided for the assembly mix).
Parameters
----------
include_fragment_plots
Either True/False/"on_error" to plot schemas of the fragments used in
the different AssemblyMix throughout the simulation.
include_part_plots
Either True/False/"on_error" to plot schemas of the parts used, possibly
with restriction sites relevant to the AssemblyMix.
include_mix_graphs
Either True/False/"on_error" to plot representations of fragment
connectivity in the AssemblyMix created during the simulation.
include_part_records
True/False to include the parts records in the simulation results (makes
for larger folders and zips, but is better for traceability).
include_assembly_plots
True/False to include assembly schemas in the reports (makes the
report generation slower, but makes it easier to check assemblies at a
glance).
show_overhangs_in_graph
If true, the AssemblyMix graph representations will display the sequence
of all fragment overhangs.
include_errors_spreadsheet
If true and there are errors, an errors spreadsheet will be added to the
report.
include_warnings_spreadsheet
If true and there are warnings, a warnings spreadsheet will be added to
the report.
include_pdf_report
If true, a PDF report file is also generated.
"""
def __init__(
self,
include_fragment_plots="on_error",
include_part_plots="on_error",
include_mix_graphs="on_error",
include_part_records=True,
include_assembly_plots=False,
show_overhangs_in_graph=True,
annotate_parts_homologies=True,
include_errors_spreadsheet=True,
include_warnings_spreadsheet=True,
include_pdf_report=False,
):
self.include_fragment_plots = include_fragment_plots
self.include_part_plots = include_part_plots
self.include_mix_graphs = include_mix_graphs
self.include_assembly_plots = include_assembly_plots
self.show_overhangs_in_graph = show_overhangs_in_graph
self.include_part_records = include_part_records
self.annotate_parts_homologies = annotate_parts_homologies
self.include_errors_spreadsheet = include_errors_spreadsheet
self.include_warnings_spreadsheet = include_warnings_spreadsheet
self.include_pdf_report = include_pdf_report
def _write_constructs_spreadsheet(self, simulation, report_root):
dataframe = simulation.compute_summary_dataframe()
target = report_root._file("%s_summary.csv" % simulation.assembly.name)
dataframe.to_csv(target.open("w"), index=False)
def _write_records(self, assembly_simulation, report_root):
if len(assembly_simulation.construct_records) > 1:
assemblies_dir = report_root._dir("assemblies")
else:
assemblies_dir = report_root
for construct_record in assembly_simulation.construct_records:
if hasattr(construct_record, "as_biopython_record"):
construct_record = construct_record.as_biopython_record()
filename = construct_record.id + ".gb"
target = assemblies_dir._file(filename)
write_record(construct_record, target, "genbank")
def _write_part_records(self, simulation, parts_records, report_root):
provided_parts_dir = report_root._dir("provided_parts_records")
for part in parts_records:
if hasattr(part, "as_biopython_record"):
part = part.as_biopython_record()
write_record(part, provided_parts_dir._file(part.id + ".gb"))
def _write_records_plots(self, assembly_simulation, report_root):
if len(assembly_simulation.construct_records) > 1:
plots_dir = report_root._dir("assemblies_plots")
else:
plots_dir = report_root
for construct_record in assembly_simulation.construct_records:
if hasattr(construct_record, "as_biopython_record"):
construct_record = construct_record.as_biopython_record()
self.plot_construct(construct_record, plots_dir)
def _write_errors_spreadsheet(self, simulation, report_root, error_type="error"):
errors = simulation.errors if error_type == "error" else simulation.warnings
if len(errors) > 0:
columns = ";".join(["assembly_name", "message", "suggestion", "data"])
all_error_rows = [
";".join([err.assembly.name, err.message, err.data_as_string(),])
for err in errors
]
filename = "%s.csv" % error_type
errors_spreadsheet = report_root._file(filename)
errors_spreadsheet.write("\n".join([columns] + all_error_rows))
[docs] def write_report(self, assembly_simulation, target):
"""Write a comprehensive report for an AssemblySimulation instance.
``target`` can be either a path to a folder, to a zip file, or
``"@memory"`` to write into a virtual zip file whose raw data is then
returned.
"""
report_root = file_tree(target, replace=True)
assembly = assembly_simulation.assembly
# The 3 next lines cover the case where connectors were added to
# the assembly, and where no assembly was found.
used_parts = assembly_simulation.list_all_parts_used()
parts = sorted(set(assembly.parts + used_parts))
repository = assembly_simulation.sequence_repository
part_records = repository.get_records(parts)
self._write_records(assembly_simulation, report_root)
if self.include_part_records:
self._write_part_records(assembly_simulation, part_records, report_root)
if self.include_assembly_plots:
self._write_records_plots(assembly_simulation, report_root)
errors_detected = len(assembly_simulation.errors) != 0
plot_options = self._get_plots_options(errors_detected)
if plot_options["parts_plots"]:
enzymes = assembly.enzymes if hasattr(assembly, "enzymes") else []
self.plot_provided_parts(
report_root=report_root, parts_records=part_records, enzymes=enzymes,
)
if plot_options["fragment_plots"]:
for mix in assembly_simulation.mixes:
mix.plot_fragments(report_root=report_root)
if plot_options["mix_graphs_plots"]:
for mix in assembly_simulation.mixes:
mix.plot_graphs(
report_root=report_root,
assembly=assembly,
with_overhangs=self.show_overhangs_in_graph,
)
if len(assembly_simulation.construct_records):
self._write_constructs_spreadsheet(assembly_simulation, report_root)
if self.include_errors_spreadsheet:
self._write_errors_spreadsheet(
assembly_simulation, report_root, error_type="error"
)
if self.include_warnings_spreadsheet:
self._write_errors_spreadsheet(
assembly_simulation, report_root, error_type="warnings"
)
if target == "@memory":
return report_root._close()
