pydna 5.5.2__py3-none-any.whl → 5.5.3__py3-none-any.whl

pydna/cre_lox.py

@@ -0,0 +1,130 @@
+# -*- coding: utf-8 -*-
+from itertools import product
+from pydna.dseqrecord import Dseqrecord
+from Bio.Data.IUPACData import ambiguous_dna_values
+from Bio.Seq import reverse_complement
+from pydna.sequence_regex import compute_regex_site, dseqrecord_finditer
+from Bio.SeqFeature import Location, SimpleLocation, SeqFeature
+from pydna.utils import shift_location
+
+# We create a dictionary to map ambiguous bases to their consensus base
+# For example, ambigous_base_dict['ACGT'] -> 'N'
+ambiguous_base_dict = {}
+for ambiguous, bases in ambiguous_dna_values.items():
+    ambiguous_base_dict["".join(sorted(bases))] = ambiguous
+
+# To handle N values
+ambiguous_base_dict["N"] = "N"
+
+# This is the original loxP sequence, here for reference
+LOXP_SEQUENCE = "ATAACTTCGTATAGCATACATTATACGAAGTTAT"
+
+loxP_sequences = [
+    # https://blog.addgene.org/plasmids-101-cre-lox
+    # loxP
+    "ATAACTTCGTATANNNTANNNTATACGAAGTTAT",
+    # PMID:12202778
+    # lox66
+    "ATAACTTCGTATANNNTANNNTATACGAACGGTA",
+    # lox71
+    "TACCGTTCGTATANNNTANNNTATACGAAGTTAT",
+]
+
+loxP_consensus = ""
+
+for pos in range(len(LOXP_SEQUENCE)):
+    all_letters = set(seq[pos] for seq in loxP_sequences)
+    key = "".join(sorted(all_letters))
+    loxP_consensus += ambiguous_base_dict[key]
+
+# We compute the regex for the forward and reverse loxP sequences
+loxP_regex = (
+    compute_regex_site(loxP_consensus),
+    compute_regex_site(reverse_complement(loxP_consensus)),
+)
+
+
+def cre_loxP_overlap(
+    x: Dseqrecord, y: Dseqrecord, _l: None = None
+) -> list[tuple[int, int, int]]:
+    """Find matching loxP sites between two sequences."""
+    out = list()
+    for pattern in loxP_regex:
+        matches_x = dseqrecord_finditer(pattern, x)
+        matches_y = dseqrecord_finditer(pattern, y)
+
+        for match_x, match_y in product(matches_x, matches_y):
+            value_x = match_x.group()
+            value_y = match_y.group()
+            if value_x[13:21] == value_y[13:21]:
+                out.append((match_x.start() + 13, match_y.start() + 13, 8))
+    # Unique values (keeping the order)
+    unique_out = []
+    for item in out:
+        if item not in unique_out:
+            unique_out.append(item)
+    return unique_out
+
+
+loxP_dict = {
+    "loxP": "ATAACTTCGTATANNNTANNNTATACGAAGTTAT",
+    "lox66": "ATAACTTCGTATANNNTANNNTATACGAACGGTA",
+    "lox71": "TACCGTTCGTATANNNTANNNTATACGAAGTTAT",
+    "loxP_mutant": "TACCGTTCGTATANNNTANNNTATACGAACGGTA",
+}
+
+
+def get_regex_dict(original_dict: dict[str, str]) -> dict[str, str]:
+    """Get the regex dictionary for the original dictionary."""
+    out = dict()
+    for site in original_dict:
+        consensus_seq = original_dict[site]
+        is_palindromic = consensus_seq == reverse_complement(consensus_seq)
+        out[site] = {
+            "forward_regex": compute_regex_site(original_dict[site]),
+            "reverse_regex": (
+                None
+                if is_palindromic
+                else compute_regex_site(reverse_complement(original_dict[site]))
+            ),
+        }
+    return out
+
+
+def find_loxP_sites(seq: Dseqrecord) -> dict[str, list[Location]]:
+    """Find all loxP sites in a sequence and return a dictionary with the name and positions of the sites."""
+
+    out = dict()
+    regex_dict = get_regex_dict(loxP_dict)
+    for site in loxP_dict:
+
+        for pattern in ["forward_regex", "reverse_regex"]:
+            # Palindromic sequences have no reverse complement
+            if regex_dict[site][pattern] is None:
+                continue
+            matches = list(dseqrecord_finditer(regex_dict[site][pattern], seq))
+            for match in matches:
+                if site not in out:
+                    out[site] = []
+                strand = 1 if pattern == "forward_regex" else -1
+                loc = SimpleLocation(match.start(), match.end(), strand)
+                loc = shift_location(loc, 0, len(seq))
+                out[site].append(loc)
+    return out
+
+
+def annotate_loxP_sites(seq: Dseqrecord) -> Dseqrecord:
+    sites = find_loxP_sites(seq)
+    for site in sites:
+        for loc in sites[site]:
+            # Don't add the same feature twice
+            if not any(
+                f.location == loc
+                and f.type == "protein_bind"
+                and f.qualifiers.get("label", []) == [site]
+                for f in seq.features
+            ):
+                seq.features.append(
+                    SeqFeature(loc, type="protein_bind", qualifiers={"label": [site]})
+                )
+    return seq

pydna/gateway.py

@@ -1,162 +1,164 @@
-#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
-# This code is part of the Python-dna distribution and governed by its
-# license.  Please see the LICENSE.txt file that should have been included
-# as part of this package.
-
-"""Assembly of sequences by Gateway recombination.
-
-Given a list of sequences (Dseqrecords), all sequences are analyzed for
-presence of att(P|B|L|R)N where N is 1,2,3 or 4.
-
-A graph is constructed where the att sites form a nodes and
-sequences separating att sites form edges.
-
-The NetworkX package is used to trace linear and circular paths through the
-graph.
-"""
-# from Bio.SeqFeature import ExactPosition as _ExactPosition
-# from Bio.SeqFeature import SimpleLocation as _SimpleLocation
-# from Bio.SeqFeature import CompoundLocation as _CompoundLocation
-# from pydna.utils import rc as _rc
-
-# from pydna._pretty import pretty_str as _pretty_str
-# from pydna.contig import Contig as _Contig
-# from pydna.common_sub_strings import common_sub_strings
-# from pydna.dseqrecord import Dseqrecord as _Dseqrecord
-# import networkx as _nx
-# from copy import deepcopy as _deepcopy
-# import itertools as _itertools
-# import logging as _logging
-
-# _module_logger = _logging.getLogger("pydna." + __name__)
-
-ambiguous_dna_regex = {
-    "A": "T",
-    "C": "G",
-    "G": "C",
-    "T": "A",
-    "M": "[ACM]",
-    "R": "[AGR]",
-    "W": "[ATW]",
-    "S": "[CGS]",
-    "Y": "[CTY]",
-    "K": "[GTK]",
-    "V": "[ACGVMSR]",
-    "H": "[ACTHMYW]",
-    "D": "[AGTDRWK]",
-    "B": "[CGTBSKY]",
-    "X": "X",
-    "N": "[ACGTBDHKMNRSVWY]",
+from Bio.Seq import reverse_complement
+from pydna.dseqrecord import Dseqrecord as _Dseqrecord
+import re
+import itertools as _itertools
+from Bio.SeqFeature import SimpleLocation, SeqFeature
+from pydna.utils import shift_location
+from pydna.sequence_regex import compute_regex_site, dseqrecord_finditer
+
+
+raw_gateway_common = {
+    "attB1": "CHWVTWTGTACAAAAAANNNG",
+    "attB2": "CHWVTWTGTACAAGAAANNNG",
+    "attB3": "CHWVTWTGTATAATAAANNNG",
+    "attB4": "CHWVTWTGTATAGAAAANNNG",
+    "attB5": "CHWVTWTGTATACAAAANNNG",
+    "attL1": "VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTACAAAAAANNNG",
+    "attL2": "VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTACAAGAAANNNG",
+    "attL3": "VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTATAATAAANNNG",
+    "attL4": "VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTATAGAAAANNNG",
+    "attL5": "VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTATACAAAANNNG",
+    "attR1": "CHWVTWTGTACAAAAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV",
+    "attR2": "CHWVTWTGTACAAGAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV",
+    "attR3": "CHWVTWTGTATAATAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV",
+    "attR4": "CHWVTWTGTATAGAAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV",
+    "attR5": "CHWVTWTGTATACAAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV",
+    "overlap_1": "twtGTACAAAaaa",
+    "overlap_2": "twtGTACAAGaaa",
+    "overlap_3": "twtGTATAATaaa",
+    "overlap_4": "twtGTATAGAaaa",
+    "overlap_5": "twtGTATACAaaa",
 }
 
-atts = """
-attP1 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT GTACAAA AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG CMASTWT AAAGYWG
-attP2 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT GTACAAG AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG CMASTWT AAAGYWG
-attP3 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT GTATAAT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG CMASTWT AAAGYWG
-attP4 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT GTATAGA AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG CMASTWT AAAGYWG
-attP5 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT GTATACA AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG CMASTWT AAAGYWG
-
-attB1 CMASTWT GTACAAA AAAGYWG AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG
-attB2 CMASTWT GTACAAG AAAGYWG AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG
-attB3 CMASTWT GTATAAT AAAGYWG AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG
-attB4 CMASTWT GTATAGA AAAGYWG AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG
-attB5 CMASTWT GTATACA AAAGYWG AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG
-
-attR1 CMASTWT GTACAAA AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT AAAGYWG
-attR2 CMASTWT GTACAAG AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT AAAGYWG
-attR3 CMASTWT GTATAAT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT AAAGYWG
-attR4 CMASTWT GTATAGA AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT AAAGYWG
-attR5 CMASTWT GTATACA AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT AAAGYWG
-
-attL1 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT GTACAAA AAAGYWG CMASTWT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG
-attL2 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT GTACAAG AAAGYWG CMASTWT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG
-attL3 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT GTATAAT AAAGYWG CMASTWT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG
-attL4 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT GTATAGA AAAGYWG CMASTWT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG
-attL5 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATKMTTTYTTATAATGCCMASTTT GTATACA AAAGYWG CMASTWT AAAGYWGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATRCTGTAAAACACAACATATSCAGTCAYWWTG
-"""
-
-
-retable = str.maketrans(ambiguous_dna_regex)
-
-for line in (line for line in atts.splitlines() if line.strip()):
-    name, *parts = line.split()
-    for part in parts:
-        part.translate(retable)
-
-
-class Gateway(object):
-    """Assembly of linear DNA fragments into linear or circular constructs.
-
-    The Assembly is meant to replace the Assembly method as it
-    is easier to use. Accepts a list of Dseqrecords (source fragments) to
-    initiate an Assembly object. Several methods are available for analysis
-    of overlapping sequences, graph construction and assembly.
-
-    Parameters
-    ----------
-    fragments : list
-        a list of Dseqrecord objects.
-    """
-
-    def __init__(self, molecules=None):
-        self.molecules = molecules
-
-
-"""
-Created on Sat Aug 21 15:41:42 2021
-
-@author: bjorn
-
-
-https://en.wikipedia.org/wiki/Cre-Lox_recombination
-
-13bp	      8bp	   13bp
-ATAACTTCGTATA-NNNTANNN-TATACGAAGTTAT
-
-
-Name	    13 bp  	        8 bp  	    13 bp
-            Recognition     Spacer      Recognition
-            Region          Region      Region
-
-Wild-Type	ATAACTTCGTATA	ATGTATGC	TATACGAAGTTAT
-lox 511	    ATAACTTCGTATA	ATGTATaC	TATACGAAGTTAT
-lox 5171	ATAACTTCGTATA	ATGTgTaC	TATACGAAGTTAT
-lox 2272	ATAACTTCGTATA	AaGTATcC	TATACGAAGTTAT
-M2	        ATAACTTCGTATA	AgaaAcca	TATACGAAGTTAT
-M3	        ATAACTTCGTATA	taaTACCA	TATACGAAGTTAT
-M7	        ATAACTTCGTATA	AgaTAGAA	TATACGAAGTTAT
-M11	        ATAACTTCGTATA	cgaTAcca	TATACGAAGTTAT
-lox 71	    TACCGTTCGTATA	NNNTANNN	TATACGAAGTTAT
-lox 66	    ATAACTTCGTATA	NNNTANNN	TATACGAACGGTA
 
-"""
-
-
-"""
-
-https://blog.addgene.org/plasmids-101-cre-lox
+raw_gateway_sites_greedy = {
+    **raw_gateway_common,
+    "attP1": "VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTACAAAAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV",
+    "attP2": "VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTACAAGAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV",
+    "attP3": "VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTATAATAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV",
+    "attP4": "VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTATAGAAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV",
+    "attP5": "VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTATACAAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV",
+}
 
-https://en.wikipedia.org/wiki/Cre-Lox_recombination
+raw_gateway_sites_conservative = {
+    **raw_gateway_common,
+    "attP1": "AAAWWAWKRWTTTWWTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATGCTTTYTTATAATGCCMASTTTGTACAAAAAAGYWGAACGAGAARCGTAAARTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATSCAGTCACTATGAAYCAACTACTTAGATGGTATTAGTGACCTGTA",
+    "attP2": "AAAWWAWKRWTTTWWTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATGCTTTYTTATAATGCCMASTTTGTACAAGAAAGYWGAACGAGAARCGTAAARTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATSCAGTCACTATGAAYCAACTACTTAGATGGTATTAGTGACCTGTA",
+    "attP3": "AAAWWAWKRWTTTWWTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATGCTTTYTTATAATGCCMASTTTGTATAATAAAGYWGAACGAGAARCGTAAARTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATSCAGTCACTATGAAYCAACTACTTAGATGGTATTAGTGACCTGTA",
+    "attP4": "AAAWWAWKRWTTTWWTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATGCTTTYTTATAATGCCMASTTTGTATAGAAAAGYWGAACGAGAARCGTAAARTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATSCAGTCACTATGAAYCAACTACTTAGATGGTATTAGTGACCTGTA",
+    "attP5": "AAAWWAWKRWTTTWWTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATGCTTTYTTATAATGCCMASTTTGTATACAAAAGYWGAACGAGAARCGTAAARTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATSCAGTCACTATGAAYCAACTACTTAGATGGTATTAGTGACCTGTA",
+}
 
-13bp	      8bp	   13bp
-ATAACTTCGTATA-NNNTANNN-TATACGAAGTTAT
+gateway_sites_greedy = {
+    k: {
+        "forward_regex": compute_regex_site(v),
+        "reverse_regex": compute_regex_site(reverse_complement(v)),
+        "consensus_sequence": v,
+    }
+    for k, v in raw_gateway_sites_greedy.items()
+}
 
+gateway_sites_conservative = {
+    k: {
+        "forward_regex": compute_regex_site(v),
+        "reverse_regex": compute_regex_site(reverse_complement(v)),
+        "consensus_sequence": v,
+    }
+    for k, v in raw_gateway_sites_conservative.items()
+}
 
-Name	    13 bp  	        8 bp  	    13 bp
-            Recognition     Spacer      Recognition
-            Region          Region      Region
+# From snapgene - ask Valerie
+primer_design_attB = {
+    "attB1": "ACAAGTTTGTACAAAAAAGCAGGCT",
+    "attB2": "ACCACTTTGTACAAGAAAGCTGGGT",
+    "attB3": "ACAACTTTGTATAATAAAGTTGTA",
+    "attB4": "ACAACTTTGTATAGAAAAGTTGTA",
+    "attB5": "ACAACTTTGTATACAAAAGTTGTA",
+}
 
-Wild-Type	ATAACTTCGTATA	ATGTATGC	TATACGAAGTTAT
-lox511	    ATAACTTCGTATA	ATGTATaC	TATACGAAGTTAT
-lox5171	    ATAACTTCGTATA	ATGTgTaC	TATACGAAGTTAT
-lox2272	    ATAACTTCGTATA	AaGTATcC	TATACGAAGTTAT
-M2	        ATAACTTCGTATA	AgaaAcca	TATACGAAGTTAT
-M3	        ATAACTTCGTATA	taaTACCA	TATACGAAGTTAT
-M7	        ATAACTTCGTATA	AgaTAGAA	TATACGAAGTTAT
-M11	        ATAACTTCGTATA	cgaTAcca	TATACGAAGTTAT
-lox71	    TACCGTTCGTATA	NNNTANNN	TATACGAAGTTAT
-lox66	    ATAACTTCGTATA	NNNTANNN	TATACGAACGGTA
 
-"""
+def gateway_overlap(
+    seqx: _Dseqrecord, seqy: _Dseqrecord, reaction: str, greedy: bool
+) -> list[tuple[int, int, int]]:
+    """
+    Find gateway overlaps. If greedy is True, it uses a more greedy consensus site to find attP sites,
+    which might give false positives
+    """
+    if reaction not in ["BP", "LR"]:
+        raise ValueError(f"Invalid overlap type: {reaction}")
+
+    gateway_sites = gateway_sites_greedy if greedy else gateway_sites_conservative
+    out = list()
+    # Iterate over the four possible att sites
+    for num in range(1, 5):
+        # Iterate over the two possible orientations
+        # The sites have to be in the same orientation (fwd + fwd or rev + rev)
+        for pattern in ["forward_regex", "reverse_regex"]:
+            # The overlap regex is the same for all types
+            overlap_regex = gateway_sites[f"overlap_{num}"][pattern]
+
+            # Iterate over pairs B, P and P, B for BP and L, R and R, L for LR
+            for site_x, site_y in zip(reaction, reaction[::-1]):
+                site_x_regex = gateway_sites[f"att{site_x}{num}"][pattern]
+                matches_x = list(dseqrecord_finditer(site_x_regex, seqx))
+                if len(matches_x) == 0:
+                    continue
+
+                site_y_regex = gateway_sites[f"att{site_y}{num}"][pattern]
+                matches_y = list(dseqrecord_finditer(site_y_regex, seqy))
+                if len(matches_y) == 0:
+                    continue
+
+                for match_x, match_y in _itertools.product(matches_x, matches_y):
+                    # Find the overlap sequence within each match, and use the
+                    # core 7 pbs that are constant
+                    overlap_x = re.search(overlap_regex, match_x.group())
+                    overlap_y = re.search(overlap_regex, match_y.group())
+
+                    # Sanity check
+                    assert (
+                        overlap_x is not None and overlap_y is not None
+                    ), "Something went wrong, no overlap found within the matches"
+
+                    out.append(
+                        (
+                            match_x.start() + overlap_x.start() + 3,
+                            match_y.start() + overlap_y.start() + 3,
+                            7,
+                        )
+                    )
+
+    return out
+
+
+def find_gateway_sites(
+    seq: _Dseqrecord, greedy: bool
+) -> dict[str, list[SimpleLocation]]:
+    """Find all gateway sites in a sequence and return a dictionary with the name and positions of the sites."""
+    gateway_sites = gateway_sites_greedy if greedy else gateway_sites_conservative
+    out = dict()
+    for site in gateway_sites:
+        if not site.startswith("att"):
+            continue
+
+        for pattern in ["forward_regex", "reverse_regex"]:
+            matches = list(dseqrecord_finditer(gateway_sites[site][pattern], seq))
+            for match in matches:
+                if site not in out:
+                    out[site] = []
+                strand = 1 if pattern == "forward_regex" else -1
+                loc = SimpleLocation(match.start(), match.end(), strand)
+                loc = shift_location(loc, 0, len(seq))
+                out[site].append(loc)
+    return out
+
+
+def annotate_gateway_sites(seq: _Dseqrecord, greedy: bool) -> _Dseqrecord:
+    sites = find_gateway_sites(seq, greedy)
+    for site in sites:
+        for loc in sites[site]:
+            seq.features.append(
+                SeqFeature(loc, type="protein_bind", qualifiers={"label": [site]})
+            )
+    return seq

pydna/parsers.py

@@ -208,3 +208,26 @@ def parse(data, ds=True):
 def parse_primers(data):
     """docstring."""
     return [_Primer(x) for x in parse(data, ds=False)]
+
+
+def parse_snapgene(file_path: str) -> list[_Dseqrecord]:
+    """Parse a SnapGene file and return a Dseqrecord object.
+
+    Parameters
+    ----------
+    file_path : str
+        The path to the SnapGene file to parse.
+
+    Returns
+    -------
+    Dseqrecord
+        The parsed SnapGene file as a Dseqrecord object.
+
+    """
+    with open(file_path, "rb") as f:
+        parsed_seq = next(_SeqIO.parse(f, "snapgene"))
+        circular = (
+            "topology" in parsed_seq.annotations.keys()
+            and parsed_seq.annotations["topology"] == "circular"
+        )
+        return [_Dseqrecord(parsed_seq, circular=circular)]

pydna/seqrecord.py

@@ -197,7 +197,7 @@ class SeqRecord(_SeqRecord):
     def translate(self):
         """docstring."""
         p = super().translate()
-        return ProteinSeqRecord(_ProteinSeq(p.seq[:-1]))
+        return ProteinSeqRecord(_ProteinSeq(p.seq))
 
     def add_colors_to_features_for_ape(self):
         """Assign colors to features.

pydna/sequence_regex.py

@@ -0,0 +1,44 @@
+# -*- coding: utf-8 -*-
+from pydna.dseqrecord import Dseqrecord as _Dseqrecord
+import re
+from Bio.Data.IUPACData import ambiguous_dna_values as _ambiguous_dna_values
+
+ambiguous_only_dna_values = {**_ambiguous_dna_values}
+for normal_base in "ACGT":
+    del ambiguous_only_dna_values[normal_base]
+
+
+def compute_regex_site(site: str) -> str:
+    """
+    Creates a regex pattern from a string that may contain degenerate bases.
+
+    Args:
+        site: The string to convert to a regex pattern.
+
+    Returns:
+        The regex pattern.
+    """
+    upper_site = site.upper()
+    for k, v in ambiguous_only_dna_values.items():
+        if len(v) > 1:
+            upper_site = upper_site.replace(k, f"[{''.join(v)}]")
+
+    # Make case insensitive
+    upper_site = f"(?i){upper_site}"
+    return upper_site
+
+
+def dseqrecord_finditer(pattern: str, seq: _Dseqrecord) -> list[re.Match]:
+    """
+    Finds all matches of a regex pattern in a Dseqrecord.
+
+    Args:
+        pattern: The regex pattern to search for.
+        seq: The Dseqrecord to search in.
+
+    Returns:
+        A list of matches.
+    """
+    query = str(seq.seq) if not seq.circular else str(seq.seq) * 2
+    matches = re.finditer(pattern, query)
+    return (m for m in matches if m.start() <= len(seq))

{pydna-5.5.2.dist-info → pydna-5.5.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pydna
-Version: 5.5.2
+Version: 5.5.3
 Summary: Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules.
 License: BSD
 Author: Björn F. Johansson
@@ -49,9 +49,9 @@ Description-Content-Type: text/markdown
 
 # ![icon](https://github.com/pydna-group/pydna/blob/master/docs/_static/banner.png?raw=true)
 
-| [![Tests & Coverage](https://github.com/pydna-group/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml/badge.svg?branch=dev_bjorn)](https://github.com/pydna-group/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml) | [![codecov](https://codecov.io/gh/BjornFJohansson/pydna/branch/master/graph/badge.svg)](https://codecov.io/gh/BjornFJohansson/pydna/branch/master) | [![PyPI version](https://badge.fury.io/py/pydna.svg)](https://badge.fury.io/py/pydna)                                                  | [![Google group : pydna](https://img.shields.io/badge/Google%20Group-pydna-blue.svg)](https://groups.google.com/g/pydna)          |
+| [![Tests & Coverage](https://github.com/pydna-group/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml/badge.svg?branch=master)](https://github.com/pydna-group/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml) | [![codecov](https://codecov.io/gh/pydna-group/pydna/branch/master/graph/badge.svg)](https://codecov.io/gh/pydna-group/pydna/branch/master) | [![PyPI version](https://badge.fury.io/py/pydna.svg)](https://badge.fury.io/py/pydna)                                                  | [![Google group : pydna](https://img.shields.io/badge/Google%20Group-pydna-blue.svg)](https://groups.google.com/g/pydna)          |
 | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------- |
-| [![Documentation Status](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml/badge.svg)](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml)                                                      | [![GitHub issues](https://img.shields.io/github/issues/BjornFJohansson/pydna.svg)](https://github.com/pydna-group/pydna/issues)                    |  [![GitHub stars](https://img.shields.io/github/stars/BjornFJohansson/pydna.svg)](https://github.com/pydna-group/pydna/stargazers) | |
+| [![Documentation Status](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml/badge.svg)](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml)                                                      | [![GitHub issues](https://img.shields.io/github/issues/pydna-group/pydna.svg)](https://github.com/pydna-group/pydna/issues)                    |  [![GitHub stars](https://img.shields.io/github/stars/pydna-group/pydna.svg)](https://github.com/pydna-group/pydna/stargazers) | |
 
 <!-- docs/index.rst-start -->
 
@@ -438,15 +438,11 @@ Feedback & suggestions are very welcome! Please create an issue with your questi
 
 If you don't have a github account, you can get in touch through the [google group](https://groups.google.com/d/forum/pydna) for pydna.
 
-Below are the instructions for developers who want to contribute to pydna. Please direct pull requests towards the `dev_bjorn` branch.
+Below are the instructions for developers who want to contribute to pydna. Please direct pull requests towards the `master` branch.
 
 ### Fork the repository and set up a dev branch 🍴
 
-Fork the entire repository (not just the `master` branch by unticking the "Copy the `master` branch only" box)
-
-![Fork](https://github.com/pydna-group/pydna/blob/master/docs/_static/create-fork.png?raw=true)
-
-Create your branch starting from `dev_bjorn`, and if your changes are related to an issue, call the branch `issue_<number>`.
+Fork the repository. Create your branch starting from `master`, and if your changes are related to an issue, call the branch `issue_<number>`.
 
 ```bash
 # Clone the repository
@@ -455,12 +451,6 @@ git clone https://github.com/<your-username>/pydna.git
 # Change to the repository directory
 cd pydna
 
-# Go to the dev_bjorn branch
-git checkout -b dev_bjorn
-
-# Pull the current version of dev_bjorn
-git pull origin dev_bjorn
-
 # Create your own branch
 git checkout -b issue_<number>
 ```
@@ -540,7 +530,7 @@ pre-commit install
 
 ### Creating a PR 🔗
 
- * From your fork, make a PR towards the branch `dev_bjorn` in the original repository.
+ * From your fork, make a PR towards the branch `master` in the original repository.
  * Mention the issue number in the PR description (e.g., `Closes #123`).
  * Remember to click the "Allow edits from maintainers" checkbox so that we can make some changes to the PR if necessary.
 
@@ -596,7 +586,7 @@ Wang, Y., Xue, H., Pourcel, C., Du, Y., & Gautheret, D. (2021).
 In Cold Spring Harbor Laboratory (p. 2021.01.17.427048). [DOI](https://doi.org/10.1101/2021.01.17.427048)
 [PubMed](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8180056)
 
-[ShareYourCloning](https://shareyourcloning.org), a web application for designing and documenting DNA cloning strategies.
+[OpenCloning](https://opencloning.org), a web application for designing and documenting DNA cloning strategies.
 
 [An Automated Protein Synthesis Pipeline with Transcriptic and Snakemake](http://blog.booleanbiotech.com/transcriptic_protein_synthesis_pipeline.html)
 

{pydna-5.5.2.dist-info → pydna-5.5.3.dist-info}/RECORD

@@ -1,15 +1,16 @@
-pydna/__init__.py,sha256=a08F6v_bfQLzTDkNEbjeSa3hadO_cuKH0mIAkoG1AtU,12867
+pydna/__init__.py,sha256=aHQGRBpQdABGgHMwN6CfDMKGvsOpCVSs2f5I5ir5DMw,12867
 pydna/_pretty.py,sha256=foRAxdL3Jiupuz7l38THBQZ7tu-5vQvLm1cKdDa7n6A,923
 pydna/_thermodynamic_data.py,sha256=9_w-97DpkbsWbJGHVijscMvUS_SFt7GxzrxspMRPZSg,10903
 pydna/all.py,sha256=xwkbR5Hn52xVfgLAXaEfIgtNwaBiGDbJFTQfa3Zi6HQ,1781
 pydna/amplicon.py,sha256=X4rCSanhlx1sPN0eAtcdAWg4Lw0WKrGQhv-cgZKtM3s,5343
 pydna/amplify.py,sha256=XRwmSMQ2d8Y379zcl56yU6rt1xWbSulWWHLqp-HRDc0,19260
 pydna/assembly.py,sha256=LM3-s3YysFvvkl1oooxoBjYLt0iMc3E1YLoqE05i8bs,19936
-pydna/assembly2.py,sha256=IN5tP5-FgdqLpIkAEKy9tXDG8x58iIgc6FUZSMr5kS0,73307
+pydna/assembly2.py,sha256=gyn-R2Jz3D6Pze27iE3IZ6JLvnqg72my9r-J34ZjWqI,98202
 pydna/codon.py,sha256=Nxa_03n2wxXKACkzi55bUN1t5xUU_DBRRwh_ZLIb9_o,2568
 pydna/common_sub_strings.py,sha256=A-gJeA2cEyxKKGQSFoC0BKvcXUGJZcnTUU7x2xlAovc,11574
 pydna/conftest.py,sha256=T5-WmHWLZH3U3ifxnbxd_oOiIFibIrkYpwNacCHlvsY,999
 pydna/contig.py,sha256=m0XV0LO2AbArPZkjyNCf8c7_b1EkXFtYwXHJVG4eTY8,8168
+pydna/cre_lox.py,sha256=sOj9R8_oFPGWs68vc4jf6LqWOXjMsVSwtJaeKl6ZF2M,4476
 pydna/crispr.py,sha256=iwu0Cjskzdb2r-In9633QIxQYKGmSNVOEM_dLK6lC54,3619
 pydna/design.py,sha256=BAoPb4M47yMkF1p4gGmbomZPFyTl0WuXkv8sLSY_Tg0,29067
 pydna/download.py,sha256=7tT8LAEy2Vg05spGfbCea_sol6pUOOBVbxOtyk2mnlQ,1085
@@ -17,7 +18,7 @@ pydna/dseq.py,sha256=2N_dXX36niJItQzN61PoVweee0xxP04_amJ3cSExAtU,54232
 pydna/dseqrecord.py,sha256=9OSuxLqcJse3aIVZCVeN7bZCyohGt7WEXnnv1qBIcB0,47983
 pydna/fakeseq.py,sha256=uxyu1PXF-sVasEqhmyhMcsbpTy84uUtubDiZuxHNb9c,1174
 pydna/fusionpcr.py,sha256=tfIfGGkNoZjg_dodcEx9wTc12aLRnC7J3g-Vg3Jg1uA,2821
-pydna/gateway.py,sha256=9OL6o9J_FQoQ5VExmHMIPDtDiJs3_4-whcS755BPCG0,8451
+pydna/gateway.py,sha256=iwNHrDIOqKl6_3Rdz7z7c8n_kcLQZuuu72oxNIjyyL8,8686
 pydna/gel.py,sha256=QE1uhnjWXLl2nXgbLs_1TWbPixgUa0-z_UR8jZaByS4,3371
 pydna/genbank.py,sha256=rH677VRklVKBpPoFRsl7Az8fZvrC8TD2lNrNoHO1wU8,8856
 pydna/genbankfile.py,sha256=ii0_RjNGnsfUThTN01c5PRLSZkQT3WlYDvoC6R6ozAA,1451
@@ -26,18 +27,19 @@ pydna/genbankrecord.py,sha256=u9RNBifT0j8rrA2bSdWajodtwm42P52_VlXsxKeOvq0,5566
 pydna/goldengate.py,sha256=LvUWAzhG9OhN1wil7osJIkjfqwBLh355a18wCZO1TvI,1778
 pydna/ladders.py,sha256=fKfWwezxQpX4qon9YCMIwchMBkGVOu8-C02xXk90J-E,3310
 pydna/ligate.py,sha256=ap8xgS4aL9cH4w38e-kpw1Ixa7DtpYF_ipezrVXiHG0,1965
-pydna/parsers.py,sha256=RFYBCKrlqWzZbRWhg5lQE3pp31KjUNAarpAgHJuUpaU,6690
+pydna/parsers.py,sha256=FW2RhZrxWX9wUYJcmt0qi1n7DZP0RfsNaXHhG0eVTWg,7319
 pydna/primer.py,sha256=k9Z_fHfBcY_rGnOtfys806rQBDtvyKwKl2ceSx3_w9A,2272
 pydna/readers.py,sha256=tKoonGlIB9ACeOMnzjhbCya1ooqhFMQIO_G36azN81E,1575
 pydna/seq.py,sha256=82gR1g2D8jfPy1So1pSJvlXYk4zkcKx_qmgvcydxth4,7579
-pydna/seqrecord.py,sha256=rzUUecmf9RkQdYHL0b9Pu8ofXM3Q6KThm-wv43jH0SA,23368
+pydna/seqrecord.py,sha256=haLp1316KQkROkQ0HkJp-RfgWN-eDyLPzTGFLjgXwHk,23363
 pydna/sequence_picker.py,sha256=Pco9IrUwNSiS0wQ5hp5FMfE9kIN9XOwXasKLF9OA6DM,1402
+pydna/sequence_regex.py,sha256=DYuAJkWm_GqEGMpd0pE-Mad_B6POUP8gwjSCFR8RfXw,1259
 pydna/threading_timer_decorator_exit.py,sha256=D91kqjKSavWDnXyc1Fo-CwPYtbmR2DjTXnBYSRXKmSA,2793
 pydna/tm.py,sha256=0r4Aqjt_qanfqR8GNvqNh8us7AKM6JvaQKqHYsswAz4,11143
 pydna/types.py,sha256=OE7iwA3b7f_T6EoBnYbRl9CFrY6OrSkAfuyY-R5kins,1389
 pydna/user_cloning.py,sha256=VSpYX1tdbcD_PzEt69Jz6Lud-yAkYMVXnzVd4v2usnE,692
 pydna/utils.py,sha256=BwBOcr2HyLAPAVdpXEEDiwJ5MeWW096EOekvfyXxbDM,25227
-pydna-5.5.2.dist-info/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
-pydna-5.5.2.dist-info/METADATA,sha256=TsRUcktnk2S-D4iZncIM54BSgQJ3XYv8EyTRfAAOgJI,25439
-pydna-5.5.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pydna-5.5.2.dist-info/RECORD,,
+pydna-5.5.3.dist-info/LICENSE.txt,sha256=u8QfcsnNXZM0UCexerK_MvyA2lPWgeGyUtSYXvLG6Oc,6119
+pydna-5.5.3.dist-info/METADATA,sha256=Orph3mLdDMwKy21DsEucxGYPyLHX9p9FimxYMiaidYU,25090
+pydna-5.5.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+pydna-5.5.3.dist-info/RECORD,,