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functional digestion
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@Gonza10V
Gonza10V committed Sep 28, 2022
1 parent 0adb6ee commit b970902
Showing 1 changed file with 60 additions and 77 deletions.
137 changes: 60 additions & 77 deletions sbol_utilities/component.py
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Original file line number Diff line number Diff line change
Expand Up @@ -718,57 +718,13 @@ def ligation(reactants:List[sbol3.Component], assembly_plan:sbol3.Component)-> L
:param reactant: DNA to be ligated as SBOL Component.
:return: A tuple of Component and Interaction.
"""
five_prime_overhangs = []
three_prime_overhangs = []
for reactant in reactants:
flank_control = [0,0]
for feature in reactant.features:
if feature.role == sbol3.SO.restriction_enzyme_five_prime_single_strand_overhang:
five_prime_overhangs.append(feature)
flank_control[0] = 1
elif feature.role == sbol3.SO.restriction_enzyme_three_prime_single_strand_overhang:
three_prime_overhangs.append(feature)
flank_control[1] = 1

if flank_control == [1,1]:
pass
elif flank_control == [0,0]:
raise ValueError(f"No flanking single strand found in reactant {reactant.identity}")
elif flank_control == [1,0]:
raise ValueError(f"No flanking single strand found in 3 prime end on reactant {reactant.identity}")
elif flank_control == [0,1]:
raise ValueError(f"No flanking single strand found in 5 prime end on reactant {reactant.identity}")
else:
raise ValueError(f"Flanking single strand does not match recognized format on reactant {reactant.identity}")

fusion_site_length = 4 # placeholder, get from reactant information
# TODO: build graph and fing all different paths or using structural pattern matching
# build graph
assembly_graph = nx.Graph()
for reactant in reactants:
assembly_graph.add_node(reactant)
for a,b in itertools.combinations(reactants,2):
reactant_a_sequence = a.sequences[0].lookup().elements
reactant_b_sequence = b.sequences[0].lookup().elements
if reactant_a_sequence[-fusion_site_length:] == reactant_b_sequence[:fusion_site_length]:
assembly_graph.add_edge(a,b, {'fusion_site':reactant_a_sequence[-fusion_site_length:]})
if reactant_a_sequence[:fusion_site_length-1] == reactant_b_sequence[-fusion_site_length:]:
assembly_graph.add_edge(a,b, {'fusion_site':reactant_b_sequence[:fusion_site_length-1]})
# find all paths that leads to an assembly product


# TODO: breadth search for all paths
'''
parts_to_combine = {reactants}
terminal_parts = set()
while parts_to_combine:
next_part = parts_to_combine.pop()
new_parts = find all combinations that can be made with elements in parts_to_combine
if new_parts:
add new_parts to parts_to_combine
else:
terminal_parts.add(next_part)
'''
# get all fusion sites
five_prime_fusion_sites = set()
three_prime_fusion_sites = set()
for r in reactants:
five_prime_fusion_sites.add(r.sequences[0].lookup().elements[:r.features[0].locations[0].end])
three_prime_fusion_sites.add(r.sequences[0].lookup().elements[r.features[0].locations[1].start:])

alignments = [[r] for r in reactants] # like [[A],[B1],[B2],[C]]] and [[A,B1,C],[B1],[B2],[C]]
used_fusion_sites = set()
final_products = [] # [[A,B1,C]]
Expand All @@ -781,53 +737,78 @@ def ligation(reactants:List[sbol3.Component], assembly_plan:sbol3.Component)-> L
alignments.pop(0)
# compare to all other alignments
for alignment in alignments:
#working_alignment_5_prime_fusion_site_length = working_alignment[0].features[0].locations[0].end
#alignment_3_prime_fusion_site_length = alignment[-1].features[0].locations[1].start
working_alignment_5_prime_fusion_site = working_alignment[0].sequences[0].lookup().elements[:working_alignment[0].features[0].locations[0].end]
working_alignment_3_prime_fusion_site = working_alignment[-1].sequences[0].lookup().elements[working_alignment[-1].features[0].locations[1].start:]
alignment_5_prime_fusion_site = alignment[0].sequences[0].lookup().elements[:alignment[0].features[0].locations[0].end]
alignment_3_prime_fusion_site = alignment[-1].sequences[0].lookup().elements[alignment[-1].features[0].locations[1].start:]
# if working alignment 5' end matches a alignment 3' end
if working_alignment[0].sequences[0].lookup().elements[:fusion_site_length-1] == alignment.sequences[0].lookup().elements[-fusion_site_length:]:
if working_alignment_5_prime_fusion_site == alignment_3_prime_fusion_site:
# if in used_fusion_sites, skip
if working_alignment[0].sequences[0].lookup().elements[:fusion_site_length-1] in used_fusion_sites:
if working_alignment_5_prime_fusion_site in used_fusion_sites:
raise ValueError(f"Fusion site {working_alignment[0].sequences[0].lookup().elements[:fusion_site_length-1]} already used")
else: used_fusion_sites.add(working_alignment_5_prime_fusion_site)
# if repeated elements pass
if(all(x in working_alignment for x in alignment)):
raise ValueError(f"Repeated elements in alignment {alignment}")
#if(all(x in working_alignment for x in alignment)):
# raise ValueError(f"Repeated elements in alignment {alignment}")

working_alignment = alignment + working_alignment
else:

working_alignment_5_prime_fusion_site = working_alignment[0].sequences[0].lookup().elements[:working_alignment[0].features[0].locations[0].end]
working_alignment_3_prime_fusion_site = working_alignment[-1].sequences[0].lookup().elements[working_alignment[-1].features[0].locations[1].start:]

# if working alignment 5' end does not matches any 3' fusion site
if working_alignment_5_prime_fusion_site not in three_prime_fusion_sites:
five_prime_end = True

# if working_alignment is closed, add to final_products
if working_alignment[0].sequences[0].lookup().elements[:fusion_site_length-1] == working_alignment.sequences[0].lookup().elements[-fusion_site_length:]:
if working_alignment_5_prime_fusion_site == working_alignment_3_prime_fusion_site:
final_products.append(working_alignment)
closed = True
break

################################################
# if alignment 3' end matches a reactant 5' end
if working_alignment[-1].sequences[0].lookup().elements[-fusion_site_length:] == alignment.sequences[0].lookup().elements[:fusion_site_length-1]:
# if working alignment 3' end matches a alignment 5' end
if working_alignment_3_prime_fusion_site == alignment_5_prime_fusion_site:
# if in used_fusion_sites, raise error
if working_alignment[-1].sequences[0].lookup().elements[-fusion_site_length:] in used_fusion_sites:
if working_alignment_3_prime_fusion_site in used_fusion_sites:
raise ValueError(f"Fusion site {working_alignment[0].sequences[0].lookup().elements[:fusion_site_length-1]} already used")
# if repeated elements, raise error
if(all(x in working_alignment for x in alignment)):
raise ValueError(f"Repeated elements in alignment {alignment}")
#if(all(x in working_alignment for x in alignment)):
# raise ValueError(f"Repeated elements in alignment {alignment}")

working_alignment = working_alignment + alignment
else:

working_alignment_5_prime_fusion_site = working_alignment[0].sequences[0].lookup().elements[:working_alignment[0].features[0].locations[0].end]
working_alignment_3_prime_fusion_site = working_alignment[-1].sequences[0].lookup().elements[working_alignment[-1].features[0].locations[1].start:]

# if working alignment 5' end does not matches any 3' fusion site
if working_alignment_3_prime_fusion_site not in five_prime_fusion_sites:
three_prime_end = True

# if working_alignment is closed, add to final_products
if working_alignment[0].sequences[0].lookup().elements[:fusion_site_length-1] == working_alignment.sequences[0].lookup().elements[-fusion_site_length:]:
if working_alignment_5_prime_fusion_site == working_alignment_3_prime_fusion_site:
final_products.append(working_alignment)
closed = True
break
elif five_prime_end and three_prime_end:
break
# if no match, add to final products
if five_prime_end and three_prime_end:
final_products.append(working_alignment)
break
else: alignments = working_alignment + alignments
break

# TODO: feed working alignment to alignments
#alignments.insert(0, working_alignment)

# use final products to build assembly product somponent
fusion_site_length = 4
products_list = []
participations = []
for composite in final_products: # a composite of the form [A,B,C]
composite_number = 1
composite_number = 0
# calculate sequence
composite_sequence_str = ""
composite_name = ""
for part in composite:
composite_sequence_str = composite_sequence_str + part.sequences[0].lookup().elements[:-fusion_site_length] #needs a version for linear
# create participations
Expand All @@ -836,23 +817,25 @@ def ligation(reactants:List[sbol3.Component], assembly_plan:sbol3.Component)-> L
assembly_plan.features.append(part_subcomponent)
part_participation = sbol3.Participation(roles=[sbol3.SBO_REACTANT], participant=part_subcomponent)
participations.append(part_participation)
composite_name = composite_name + part.name
# create dna componente and sequence
composite_component, composite_seq = dna_component_with_sequence(f'composite_{composite_number}', composite_sequence_str) # **kwarads use in future?
composite_component.types.append()
composite_component, composite_seq = dna_component_with_sequence(f'composite_{composite_number}_{composite_name}', composite_sequence_str) # **kwarads use in future?
#composite_component.types.append()
composite_component.roles.append(sbol3.SO_ENGINEERED_REGION)
composite_component.features = composite
# fix order of features
composite_component.constraints.append(sbol3.Constraint(sbol3.SBOL_MEETS, composite_component.features[composite_number-1], composite_component.features[composite_number]))
#composite_component.features = composite
# TODO fix order of features
#composite_component.constraints.append(sbol3.Constraint(sbol3.SBOL_MEETS, composite_component.features[composite_number-1], composite_component.features[composite_number]))
# add product participation
composite_subcomponent = sbol3.SubComponent(composite_component)
participations.append(sbol3.Participation(roles=[sbol3.SBO_PRODUCT], participant=composite_subcomponent))
#composite_subcomponent = sbol3.SubComponent(composite_component)
#participations.append(sbol3.Participation(roles=[sbol3.SBO_PRODUCT], participant=composite_subcomponent))
# create interactions
assembly_plan.interactions.append(sbol3.Interaction(types=[tyto.SBO.conversion], participations=participations))
#assembly_plan.interactions.append(sbol3.Interaction(types=[tyto.SBO.conversion], participations=participations))
products_list.append([composite_component, composite_seq])
composite_number += 1
#create preceed constrain
#create composite part or part in backbone
#add interactions to assembly_plan
#add participations to assembly_plan

return products_list

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