Module crecombio.crecombio
View Source
import re
from Bio.Seq import Seq
SITES = {
"Flp": {
"seq": Seq("GAAGTTCCTATTCtctagaaaGtATAGGAACTTC".upper()),
"5p": Seq("GAAGTTCCTATTC"),
"3p": Seq("tctagaaaGtATAGGAACTTC".upper()),
},
"Cre": {"seq": Seq("ATAACTTCGTATAATGTATGCTATACGAAGTTAT")},
"Cre_lox_511": {"seq": Seq("ATAACTTCGTATAATGTATACTATACGAAGTTAT")},
"Cre_lox_5171": {"seq": Seq("ATAACTTCGTATAATGTGTACTATACGAAGTTAT")},
"Cre_lox_2272": {"seq": Seq("ATAACTTCGTATAAAGTATCCTATACGAAGTTAT")},
"Cre_M2": {"seq": Seq("ATAACTTCGTATAAGAAACCATATACGAAGTTAT")},
"Cre_M3": {"seq": Seq("ATAACTTCGTATATAATACCATATACGAAGTTAT")},
"Cre_M7": {"seq": Seq("ATAACTTCGTATAAGATAGAATATACGAAGTTAT")},
"Cre_M11": {"seq": Seq("ATAACTTCGTATACGATACCATATACGAAGTTAT")},
}
def recombine(sequences, recombinase="Flp"):
"""Simulate recombination and return sequences.
**Parameters**
**sequences**
> List of one or two Biopython SeqRecord objects (`list`).
**recombinases**
> Recombinase name (`str`). Default Flp.
"""
if len(sequences) == 1:
return recombine_one_sequence(sequences, recombinase)
if len(sequences) == 2:
return recombine_two_sequences(sequences, recombinase)
else:
raise Exception("Only 1- or 2-sequence recombination is supported")
def recombine_one_sequence(sequences, recombinase="Flp"):
"""Simulate recombination of one sequence."""
recombined_sequences = []
for sequence in sequences:
site = SITES[recombinase]["seq"]
matches, rc_matches = count_number_of_sites(sequence, site)
if (len(matches) + len(rc_matches)) != 2:
raise Exception("The sequence must contain 2 recombinase sites")
# Excision
if len(matches) == 2:
new_sequence = sequence[: matches[0]] + sequence[matches[1] :]
recombined_sequences += [new_sequence]
# Excision on reverse strand
if len(rc_matches) == 2:
new_sequence = sequence[: matches[0]] + sequence[matches[1] :]
recombined_sequences += [new_sequence]
# Inversion
if len(matches) == 1 and len(rc_matches) == 1:
if matches[0] > rc_matches[0]:
raise Exception(
"Orientation incorrect: reverse complement of recombination site is"
" before the site."
)
# extend to circular sequences later
inside_sequence = sequence[
(matches[0] + len(site)) : rc_matches[0]
] # added length to not include the site
inverted_sequence = inside_sequence.reverse_complement()
left_part = sequence[: matches[0] + len(site)]
right_part = sequence[rc_matches[0] :]
new_sequence = left_part + inverted_sequence + right_part
recombined_sequences += [new_sequence]
return recombined_sequences
def recombine_two_sequences(sequences, recombinase="Flp"):
"""Simulate recombination of two sequences."""
seq0 = sequences[0]
seq1 = sequences[1]
site = SITES[recombinase]["seq"]
seq0_matches, seq0_rc_matches = count_number_of_sites(seq0, site)
seq1_matches, seq1_rc_matches = count_number_of_sites(seq1, site)
if len(seq0_rc_matches) != 0 or len(seq1_rc_matches) != 0:
print(
"Simulating recombination of reverse complement sites are not implemented "
"yet and these sites are ignored"
)
recombined_sequences = []
if len(seq0_matches) == 1 and len(seq1_matches) == 1:
# Translocate
seq0_left_part = seq0[: seq0_matches[0]]
seq0_right_part = seq0[seq0_matches[0] :] # includes the site
seq1_left_part = seq1[: seq1_matches[0]]
seq1_right_part = seq1[seq1_matches[0] :] # includes the site
seq2 = seq0_left_part + seq1_right_part
seq3 = seq1_left_part + seq0_right_part
recombined_sequences += [seq2, seq3]
elif len(seq0_matches) == 1 and len(seq1_matches) == 2:
# Insert from seq1 to seq0
donor = seq1
acceptor = seq0
donor_matches = seq1_matches
acceptor_matches = seq0_matches
new_donor = donor[: donor_matches[0]] + donor[donor_matches[1] :]
excised_seq = donor[donor_matches[0] : donor_matches[1]]
new_acceptor = (
acceptor[: acceptor_matches[0]]
+ excised_seq
+ acceptor[acceptor_matches[0] :]
)
recombined_sequences += [new_acceptor, new_donor]
elif len(seq0_matches) == 2 and len(seq1_matches) == 1:
# Insert from seq0 to seq1
donor = seq0
acceptor = seq1
donor_matches = seq0_matches
acceptor_matches = seq1_matches
# Same code as above:
new_donor = donor[: donor_matches[0]] + donor[donor_matches[1] :]
excised_seq = donor[donor_matches[0] : donor_matches[1]]
new_acceptor = (
acceptor[: acceptor_matches[0]]
+ excised_seq
+ acceptor[acceptor_matches[0] :]
)
recombined_sequences += [new_acceptor, new_donor]
elif len(seq0_matches) == 2 and len(seq1_matches) == 2:
raise Exception("Both sequences have 2 recombination sites")
else:
raise Exception(
"The number of recombination sites must be 1 or 2 in each sequence"
)
return recombined_sequences
def count_number_of_sites(sequence, site):
"""Count the number of recombination sites in a sequence.
**Parameters**
**sequence**
> A Biopython SeqRecord object.
**site**
> The site sequence (`str`).
"""
matches = [
m.start() for m in re.finditer(re.escape(str(site)), str(sequence.seq).upper())
]
rc_matches = [
m.start()
for m in re.finditer(
re.escape(str(site.reverse_complement())), str(sequence.seq).upper()
)
]
return matches, rc_matches
Variables
SITES
Functions
count_number_of_sites
def count_number_of_sites(
sequence,
site
)
Count the number of recombination sites in a sequence.
Parameters
sequence
A Biopython SeqRecord object.
site
The site sequence (
str).
View Source
def count_number_of_sites(sequence, site):
"""Count the number of recombination sites in a sequence.
**Parameters**
**sequence**
> A Biopython SeqRecord object.
**site**
> The site sequence (`str`).
"""
matches = [
m.start() for m in re.finditer(re.escape(str(site)), str(sequence.seq).upper())
]
rc_matches = [
m.start()
for m in re.finditer(
re.escape(str(site.reverse_complement())), str(sequence.seq).upper()
)
]
return matches, rc_matches
recombine
def recombine(
sequences,
recombinase='Flp'
)
Simulate recombination and return sequences.
Parameters
sequences
List of one or two Biopython SeqRecord objects (
list).
recombinases
Recombinase name (
str). Default Flp.
View Source
def recombine(sequences, recombinase="Flp"):
"""Simulate recombination and return sequences.
**Parameters**
**sequences**
> List of one or two Biopython SeqRecord objects (`list`).
**recombinases**
> Recombinase name (`str`). Default Flp.
"""
if len(sequences) == 1:
return recombine_one_sequence(sequences, recombinase)
if len(sequences) == 2:
return recombine_two_sequences(sequences, recombinase)
else:
raise Exception("Only 1- or 2-sequence recombination is supported")
recombine_one_sequence
def recombine_one_sequence(
sequences,
recombinase='Flp'
)
Simulate recombination of one sequence.
View Source
def recombine_one_sequence(sequences, recombinase="Flp"):
"""Simulate recombination of one sequence."""
recombined_sequences = []
for sequence in sequences:
site = SITES[recombinase]["seq"]
matches, rc_matches = count_number_of_sites(sequence, site)
if (len(matches) + len(rc_matches)) != 2:
raise Exception("The sequence must contain 2 recombinase sites")
# Excision
if len(matches) == 2:
new_sequence = sequence[: matches[0]] + sequence[matches[1] :]
recombined_sequences += [new_sequence]
# Excision on reverse strand
if len(rc_matches) == 2:
new_sequence = sequence[: matches[0]] + sequence[matches[1] :]
recombined_sequences += [new_sequence]
# Inversion
if len(matches) == 1 and len(rc_matches) == 1:
if matches[0] > rc_matches[0]:
raise Exception(
"Orientation incorrect: reverse complement of recombination site is"
" before the site."
)
# extend to circular sequences later
inside_sequence = sequence[
(matches[0] + len(site)) : rc_matches[0]
] # added length to not include the site
inverted_sequence = inside_sequence.reverse_complement()
left_part = sequence[: matches[0] + len(site)]
right_part = sequence[rc_matches[0] :]
new_sequence = left_part + inverted_sequence + right_part
recombined_sequences += [new_sequence]
return recombined_sequences
recombine_two_sequences
def recombine_two_sequences(
sequences,
recombinase='Flp'
)
Simulate recombination of two sequences.
View Source
def recombine_two_sequences(sequences, recombinase="Flp"):
"""Simulate recombination of two sequences."""
seq0 = sequences[0]
seq1 = sequences[1]
site = SITES[recombinase]["seq"]
seq0_matches, seq0_rc_matches = count_number_of_sites(seq0, site)
seq1_matches, seq1_rc_matches = count_number_of_sites(seq1, site)
if len(seq0_rc_matches) != 0 or len(seq1_rc_matches) != 0:
print(
"Simulating recombination of reverse complement sites are not implemented "
"yet and these sites are ignored"
)
recombined_sequences = []
if len(seq0_matches) == 1 and len(seq1_matches) == 1:
# Translocate
seq0_left_part = seq0[: seq0_matches[0]]
seq0_right_part = seq0[seq0_matches[0] :] # includes the site
seq1_left_part = seq1[: seq1_matches[0]]
seq1_right_part = seq1[seq1_matches[0] :] # includes the site
seq2 = seq0_left_part + seq1_right_part
seq3 = seq1_left_part + seq0_right_part
recombined_sequences += [seq2, seq3]
elif len(seq0_matches) == 1 and len(seq1_matches) == 2:
# Insert from seq1 to seq0
donor = seq1
acceptor = seq0
donor_matches = seq1_matches
acceptor_matches = seq0_matches
new_donor = donor[: donor_matches[0]] + donor[donor_matches[1] :]
excised_seq = donor[donor_matches[0] : donor_matches[1]]
new_acceptor = (
acceptor[: acceptor_matches[0]]
+ excised_seq
+ acceptor[acceptor_matches[0] :]
)
recombined_sequences += [new_acceptor, new_donor]
elif len(seq0_matches) == 2 and len(seq1_matches) == 1:
# Insert from seq0 to seq1
donor = seq0
acceptor = seq1
donor_matches = seq0_matches
acceptor_matches = seq1_matches
# Same code as above:
new_donor = donor[: donor_matches[0]] + donor[donor_matches[1] :]
excised_seq = donor[donor_matches[0] : donor_matches[1]]
new_acceptor = (
acceptor[: acceptor_matches[0]]
+ excised_seq
+ acceptor[acceptor_matches[0] :]
)
recombined_sequences += [new_acceptor, new_donor]
elif len(seq0_matches) == 2 and len(seq1_matches) == 2:
raise Exception("Both sequences have 2 recombination sites")
else:
raise Exception(
"The number of recombination sites must be 1 or 2 in each sequence"
)
return recombined_sequences