def test_autoselect_connectors():
data_root = flametree.file_tree(".").tests.data.select_connectors
parts = [
dc.load_record(f._path, topology="circular", id=f._name_no_extension)
for f in data_root.parts_missing_connectors._all_files
if f._extension == "gb"
]
connectors = [
dc.load_record(f._path, topology="circular", id=f._name_no_extension)
for f in data_root.connectors._all_files if f._extension == "gb"
]
mix = dc.RestrictionLigationMix(parts, enzyme="BsmBI")
selected_connectors = mix.autoselect_connectors(connectors)
assert sorted([c.id for c in selected_connectors]) == sorted([
"conn J-K",
"conn L-N",
"conn R-W",
"conn W-Z",
"conn_a_b",
"conn D-F",
])
import flametree # for getting/writing files and folders
from dnacauldron import RestrictionLigationMix, load_record, write_record
root = flametree.file_tree(".")
parts = [
load_record(f._path, topology="circular")
for f in root.data.assemblies._all_files
]
mix = RestrictionLigationMix(parts, enzyme="BsmBI")
assemblies_records = mix.compute_circular_assemblies()
output_folder = root._dir("output_data")._dir("combinatorial_assemblies")
for i, record in enumerate(assemblies_records):
output = output_folder._file("assembly_%03d.gb" % i)
write_record(record, output, "genbank")
print(
"%d combinatorial assembly genbanks written in output_data/assemblies"
% (i + 1)
)
import flametree # for getting/writing files and folders
from Bio import SeqIO # for exporting to Genbank
from dnacauldron import full_assembly_report, load_record
root = flametree.file_tree(".")
parts = [
load_record(f._path, linear=False, id=f._name_no_extension)
for f in root.data.assemblies._all_files
]
target = root._dir('output_data')._dir('report')._path
full_assembly_report(parts,
target=target,
enzyme="BsmBI",
max_assemblies=40,
fragments_filters='auto',
assemblies_prefix='asm')
print("Your report is ready at 'output_data/report/'")
import flametree # for getting/writing files and folders
from dnacauldron import RestrictionLigationMix, load_record, write_record
root = flametree.file_tree('.')
parts = [
load_record(f._path, linear=False)
for f in root.data.assemblies._all_files
]
mix = RestrictionLigationMix(parts, enzyme='BsmBI')
assemblies_records = mix.compute_circular_assemblies()
output_folder = root._dir('output_data')._dir('combinatorial_assemblies')
for i, record in enumerate(assemblies_records):
output = output_folder._file("assembly_%03d.gb" % i)
write_record(record, output, "genbank")
print ("%d combinatorial assembly genbanks written in output_data/assemblies"
% (i + 1))
import dnacauldron as dc
import os
parts_dir = os.path.join("data", "assemblies")
records_dict = {
filename.split('.')[0]: dc.load_record(
os.path.join(parts_dir, filename),
topology="circular",
id=filename.split('.')[0],
)
for filename in os.listdir(parts_dir)
}
constructs = {
"C1": ["receptor", "partA", "partB", "partC"],
"C2": ["receptor", "partA2", "partB2", "partC"],
"C3": ["receptor", "partA", "partA2", "partB", "partC"],
}
part_names = set([p for parts in constructs.values() for p in parts])
parts = {name: records_dict[name] for name in part_names}
plan = [
(construct, [parts[p] for p in construct_parts])
for construct, construct_parts in constructs.items()
]
dc.full_assembly_plan_report(
plan,
target=os.path.join("output_data", "report.zip"),
enzyme="autoselect",
assert_single_assemblies=False,
fail_silently=True,
)
import os
import pytest
import matplotlib
matplotlib.use("Agg")
import dnacauldron as dc
import flametree
records_dict = {
name: dc.load_record(
os.path.join("tests", "data", "assemblies", name + ".gb"),
id=name,
topology="circular",
)
for name in (
"partA",
"partA2",
"partB",
"partB2",
"partC",
"receptor",
"connector_A2C",
)
}
def test_filters():
to_record = dc.sequence_to_biopython_record
filter1 = dc.NoRestrictionSiteFilter("BsmBI")
assert filter1(to_record("ATGATGATG"))
import os
from dnacauldron import load_record
import flametree
data_path = os.path.join("app", "data")
data_dir = flametree.file_tree(data_path)
#
# with open(data_path, "r") as f:
# DATA = f.read()
connector_records = [
load_record(f._path, linear=False, id=f._name_no_extension)
for f in data_dir.genbank.connectors._all_files if f._extension == "gb"
]
backbone = load_record(data_dir.genbank.hc_amp_backbone_gb._path,
linear=False,
id='hc_amp_backbone')
backbone.is_backbone = True
"""
"""
from dnacauldron import load_record, insert_parts_on_backbones, BackboneChoice
import flametree # for getting/writing files and folders
root = flametree.file_tree('.')
output_dir = root._dir('output_data')._dir('backbone_autoselection')
# load lists of genbanks: one list for parts, one list for potential backbones
part_records = [
load_record(f._path, topology='circular', id=f._name_no_extension)
for f in root.data.assemblies._all_files
if f._name_no_extension in ['partA', 'partB']
]
backbone_records = [
load_record(f._path, topology='circular', id=f._name_no_extension)
for f in root.data.backbones._all_files
]
choices = insert_parts_on_backbones(part_records,
backbone_records,
process_parts_with_backbone=True)
dataframe = BackboneChoice.list_to_infos_spreadsheet(choices)
dataframe.to_excel(output_dir._file('summary.xls')._path, index=False)
BackboneChoice.write_final_records(choices, output_dir._dir("records")._path)