opencloning 0.4.8__py3-none-any.whl → 0.5__py3-none-any.whl

{opencloning-0.4.8.dist-info → opencloning-0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: opencloning
-Version: 0.4.8
+Version: 0.5
 Summary: Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others.
 License: MIT
 License-File: LICENSE
@@ -17,14 +17,13 @@ Requires-Dist: beautifulsoup4 (>=4.11.1,<5.0.0)
 Requires-Dist: biopython (>=1.85,<2.0)
 Requires-Dist: fastapi
 Requires-Dist: httpx (>=0.28.1,<0.29.0)
-Requires-Dist: opencloning-linkml (==0.4.4)
 Requires-Dist: openpyxl (>=3.1.5,<4.0.0)
 Requires-Dist: packaging (>=25.0,<26.0)
 Requires-Dist: pairwise-alignments-to-msa (>=0.1.1,<0.2.0)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
-Requires-Dist: primer3-py (==2.2.0)
+Requires-Dist: primer3-py (>=2.3,<3.0)
 Requires-Dist: pydantic (>=2.7.1,<3.0.0)
-Requires-Dist: pydna (==5.5.2)
+Requires-Dist: pydna (>=5.5.5,<6.0.0)
 Requires-Dist: python-multipart
 Requires-Dist: pyyaml (>=6.0.2,<7.0.0)
 Requires-Dist: regex (>=2024.11.6,<2025.0.0)
@@ -47,9 +46,9 @@ Read [main project readme](https://github.com/manulera/OpenCloning) first.
 
 This API provides a series of entry points. The API documentation can be accessed [here](https://api.opencloning.org/docs). You can use the documentation page to try some request directly on the browser. Otherwise, the API is open for you to make requests from a python script or command line at: [https://api.opencloning.org/](https://api.opencloning.org/).
 
-## Scripting
+## Scripting with pydna
 
-The API functions can also be used to write python scripts to automate cloning. See the [scripting examples](examples/scripting) for more information.
+You can write python scripts to automate cloning using the python library [pydna](https://github.com/pydna-group/pydna), which is now integrated with the OpenCloning data model. See [the documentation](https://github.com/pydna-group/pydna/blob/master/docs/notebooks/history.ipynb) for how to get started.
 
 ## Migrating between model versions and fixing model bugs
 
@@ -117,7 +116,7 @@ docker run -d --name backendcontainer -p 8000:8000 manulera/opencloningbackend
 
 ```
 
-If you don't want to download the repository and build the image, you can fetch the latest image from dockerhub (same image that is used in [https://api.opencloning.org/](https://api.opencloning.org/))
+If you don't want to download the repository and build the image, you can fetch the latest image from dockerhub.
 
 ```bash
 docker pull manulera/opencloningbackend
@@ -167,7 +166,7 @@ pytest -v -ks
 ### Ping a particular library version from github:
 
 ```
-poetry add git+https://github.com/BjornFJohansson/pydna#4fd760d075f77cceeb27969e017e04b42f6d0aa3
+poetry add git+https://github.com/pydna-group/pydna#4fd760d075f77cceeb27969e017e04b42f6d0aa3
 ```
 
 When installing the last version, sometimes poetry may not be able to access the latest version
@@ -188,3 +187,14 @@ RECORD_STUBS=1 uvicorn opencloning.main:app --reload --reload-exclude='.venv'
 
 This will record the stubs (requests and responses) in the `stubs` folder.
 
+
+### Catalogs
+
+Catalogs are used to map ids to urls for several plasmid collections. They are stored in the `src/opencloning/catalogs` folder.
+
+To update the catalogs, run the following command:
+
+```bash
+poetry run python scripts/update_catalogs.py
+```
+

opencloning-0.5.dist-info/RECORD

@@ -0,0 +1,51 @@
+opencloning/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+opencloning/_version.py,sha256=6QbWXLSZypjtWL_CwJFHH4dzMRK3AUH4B0YudzvGz9s,200
+opencloning/api_config_utils.py,sha256=inAXPGYNDz-DuEoSqitImj0Vv5TpQSbMZH9D3dQb5P0,4319
+opencloning/app_settings.py,sha256=O67vY7TxyKsXepOxUNc_O0JO70lf7tEL9cqIMsiTXWE,3220
+opencloning/batch_cloning/__init__.py,sha256=uDxAa45g30_S6dJScNMlIxubQXlLRUsWoLX4S4y-l88,244
+opencloning/batch_cloning/index.html,sha256=HDqPHrJxrrKfGmy_dwYHhOsdUgZHHIch7Z0ey8qyvZI,1332
+opencloning/batch_cloning/pombe/__init__.py,sha256=dVbRBba4ZcmA1x4eEn7I5kndDImQVT6-K-iqIGaDi3c,3343
+opencloning/batch_cloning/pombe/index.html,sha256=3YchoKGpcKDfvTOW1Rdih4PkbZIkMjKIQ0PaVXfV3e8,8348
+opencloning/batch_cloning/pombe/pombe_clone.py,sha256=BwnEGkz9skbIqR-W0Y1iB3wYgWH35hADp0PcUTaXKUk,3985
+opencloning/batch_cloning/pombe/pombe_gather.py,sha256=qI-biMZGLxVDV-vOf3sT6bS1BawtTihZNcSYNlnnEi8,2432
+opencloning/batch_cloning/pombe/pombe_get_primers.py,sha256=nrn6V4_l8FWWfqS4WU3qPt95KwzvCXxETh8E-zWbRhM,3968
+opencloning/batch_cloning/pombe/pombe_summary.py,sha256=GkmKZpR3fIBZd9HzyihZpITAoXgUiKe9W5l0GyLk-aU,4691
+opencloning/batch_cloning/ziqiang_et_al2024/__init__.py,sha256=PPfNUth03WWeiAwlPCPD7_uTJpgWybrUpgTTkXN_jf0,7162
+opencloning/batch_cloning/ziqiang_et_al2024/index.html,sha256=EDncANDhhQkhi5FjnnAP6liHkG5srf4_Y46IrnMUG5g,4607
+opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json,sha256=uR1emjNhCDk6uYCJC4MJwz9MJ9U5RQZk9j5cKPbqNXE,156906
+opencloning/bug_fixing/README.md,sha256=eak5x1NTyTxsklaZ1BzB3RYH26MC_2gNuH-gHvuNpKY,4441
+opencloning/bug_fixing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+opencloning/bug_fixing/backend_v0_3.py,sha256=_kxYPcUmBFGL1WEwtpl6ySwSSN0WRk9qZwX2Kc4eAUs,4608
+opencloning/catalogs/__init__.py,sha256=hHalYzJimaHWM39RPAMGduSxSWpjHy8UBqO-utOmp88,1103
+opencloning/catalogs/igem2024.yaml,sha256=CWayosovGycGCfDG-EOgPRjOMUYsDCsFy5DoHGJGwc4,49247
+opencloning/catalogs/openDNA_collections.yaml,sha256=JPnPLJd9ynJkqJAumu0f7-E5E0WSDN2pjB7rNa3wJLA,38655
+opencloning/catalogs/readme.txt,sha256=SPBPLfqszGH0zl7EZYddNwi9nE90or82o8aHNMscSkw,87
+opencloning/catalogs/seva.tsv,sha256=FFGZDDgsExYke1S0g_KCzM5YL680_RS-1XNEJbiqFJo,16125
+opencloning/catalogs/snapgene.yaml,sha256=Zi0i4l9KBOhoHnr7i2nYWD58IIYgBbEaNF5m4qzm2ks,47359
+opencloning/dna_functions.py,sha256=vyy2UDyYj3IfVmWf1z07j8T7D53JM-wFQFawcLzZt-k,15967
+opencloning/dna_utils.py,sha256=n_XRBr9xeEQSoMUWdgH7UigZN2KtU7AxmIwW18aFQdY,6814
+opencloning/ebic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+opencloning/ebic/primer_design.py,sha256=e_PkEhnlkeV7D3iCeDL8s1p-FkNWj17zWNaq-x9Uz8E,3149
+opencloning/ebic/primer_design_settings.py,sha256=OnFsuh0QCvplUEPXLZouzRo9R7rm4nLbcd2LkDCiIDM,1896
+opencloning/endpoints/annotation.py,sha256=_jQGvwcP-LvoLJKaRG2_YyMLyOzk1R9lUlYNHFc7afY,2126
+opencloning/endpoints/assembly.py,sha256=e6PFNp0ZmAQ7niI54vAZkuTgjTg1NIf0vCnVfebF184,13373
+opencloning/endpoints/endpoint_utils.py,sha256=KIbYA-XPFArHzVTQ8RfxDR4eI3WypOZPJx64_GmjGHY,2061
+opencloning/endpoints/external_import.py,sha256=IdhI1mBvBF77v6DB4Sfc5-RSzW90MzGjTc-zX7aeaxI,19671
+opencloning/endpoints/no_assembly.py,sha256=dOyfh_nfQOmnJx6Vwhwo7EBIIbMRwGf_Ap_VsjSQc40,4031
+opencloning/endpoints/no_input.py,sha256=1NSiuyS2zWwK3Ae34tFChhqEZ7645w75ibNW9RREYVw,3752
+opencloning/endpoints/other.py,sha256=e_GXJDnqQFREU9GcOruI-8yQJpK-eVtDH1ZiVPL7WQU,4028
+opencloning/endpoints/primer_design.py,sha256=2XSflQXQ1vOqY6vyvalrOU3baC2-fn-oSV5294c5cXI,13017
+opencloning/get_router.py,sha256=l2DXaTbeL2tDqlnVMlcewutzt1sjaHlxku1X9HVUwJk,252
+opencloning/http_client.py,sha256=9f0mqYPwQmWr0B6hMSoYT80g4RT2itKA2iokAknY5yY,1239
+opencloning/main.py,sha256=l9PrPBMtGMEWxAPiPWR15Qv2oDNnRoNd8H8E3bZW6Do,3750
+opencloning/ncbi_requests.py,sha256=jO3UWlGMENE3YPDCfo-pZWO5iJa1C0x7rahIf0cLCRk,8936
+opencloning/primer3_functions.py,sha256=R29jic_tb7qhXnDb4RGCx2xaViVCnxTyaVU89KMUIjQ,3584
+opencloning/primer_design.py,sha256=vHi4cBjxEOimzEABvt0sEcDZeXvZLkpnj7k9K7qu9qw,9249
+opencloning/pydantic_models.py,sha256=cKXRHQyPdQDxkdzEwKgwvmQy0UjFjDVFR-eKIsBSZbE,2964
+opencloning/request_examples.py,sha256=rg-v9a5ttzwu5tKY5h3tiT_kVkIZOicS8c01MxrEcEY,2653
+opencloning/temp_functions.py,sha256=wRh26uW_JT9sy3070jIizTT82CE_hS8-GRW3vXEd1GQ,2029
+opencloning/utils.py,sha256=0Lvw1h1AsUJTK2b9mNzYVi_DBeWmWCFA5dIPl_gERcI,1479
+opencloning-0.5.dist-info/METADATA,sha256=4ZQGH31rO4f_p9WIxTpu7UfKK8H6D1D_YilCscz1XUc,9501
+opencloning-0.5.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
+opencloning-0.5.dist-info/licenses/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
+opencloning-0.5.dist-info/RECORD,,

{opencloning-0.4.8.dist-info → opencloning-0.5.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.2.1
+Generator: poetry-core 2.3.0
 Root-Is-Purelib: true
 Tag: py3-none-any

opencloning/cre_lox.py

@@ -1,116 +0,0 @@
-from itertools import product
-from pydna.dseqrecord import Dseqrecord
-from Bio.Data.IUPACData import ambiguous_dna_values
-from Bio.Seq import reverse_complement
-from .dna_utils 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 gateway 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

opencloning/gateway.py

@@ -1,154 +0,0 @@
-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 .dna_utils 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',
-}
-
-
-raw_gateway_sites_greedy = {
-    **raw_gateway_common,
-    'attP1': 'VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTACAAAAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV',
-    'attP2': 'VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTACAAGAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV',
-    'attP3': 'VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTATAATAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV',
-    'attP4': 'VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTATAGAAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV',
-    'attP5': 'VAAWWAWKRWTTTWWTTYGACTGATAGTGACCTGTWCGTYGMAACAVATTGATRAGCAATKMTTTYYTATAWTGHCMASTWTGTATACAAAAGYWGARCGAGAARCGTAARRTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATRCTGTAARACACAACATATBCAGTCV',
-}
-
-raw_gateway_sites_conservative = {
-    **raw_gateway_common,
-    'attP1': 'AAAWWAWKRWTTTWWTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATGCTTTYTTATAATGCCMASTTTGTACAAAAAAGYWGAACGAGAARCGTAAARTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATSCAGTCACTATGAAYCAACTACTTAGATGGTATTAGTGACCTGTA',
-    'attP2': 'AAAWWAWKRWTTTWWTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATGCTTTYTTATAATGCCMASTTTGTACAAGAAAGYWGAACGAGAARCGTAAARTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATSCAGTCACTATGAAYCAACTACTTAGATGGTATTAGTGACCTGTA',
-    'attP3': 'AAAWWAWKRWTTTWWTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATGCTTTYTTATAATGCCMASTTTGTATAATAAAGYWGAACGAGAARCGTAAARTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATSCAGTCACTATGAAYCAACTACTTAGATGGTATTAGTGACCTGTA',
-    'attP4': 'AAAWWAWKRWTTTWWTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATGCTTTYTTATAATGCCMASTTTGTATAGAAAAGYWGAACGAGAARCGTAAARTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATSCAGTCACTATGAAYCAACTACTTAGATGGTATTAGTGACCTGTA',
-    'attP5': 'AAAWWAWKRWTTTWWTTTGACTGATAGTGACCTGTTCGTTGCAACAMATTGATRAGCAATGCTTTYTTATAATGCCMASTTTGTATACAAAAGYWGAACGAGAARCGTAAARTGATATAAATATCAATATATTAAATTAGAYTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATSCAGTCACTATGAAYCAACTACTTAGATGGTATTAGTGACCTGTA',
-}
-
-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()
-}
-
-# From snapgene - ask Valerie
-primer_design_attB = {
-    'attB1': 'ACAAGTTTGTACAAAAAAGCAGGCT',
-    'attB2': 'ACCACTTTGTACAAGAAAGCTGGGT',
-    'attB3': 'ACAACTTTGTATAATAAAGTTGTA',
-    'attB4': 'ACAACTTTGTATAGAAAAGTTGTA',
-    'attB5': 'ACAACTTTGTATACAAAAGTTGTA',
-}
-
-
-def gateway_overlap(seqx: _Dseqrecord, seqy: _Dseqrecord, reaction: str, greedy: bool) -> list[tuple[int, int, int]]:
-    """Find gateway overlaps"""
-    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

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