From dc115d1022235857c019245dc3b6a6766264ab8f Mon Sep 17 00:00:00 2001 From: Larry Babb Date: Wed, 20 Mar 2024 14:52:01 -0400 Subject: [PATCH] Add support for mito `m.` in translate_from (#362) --- setup.cfg | 2 +- src/ga4gh/vrs/extras/translator.py | 47 ++- tests/extras/cassettes/test_from_beacon.yaml | 51 ++- tests/extras/cassettes/test_from_gnomad.yaml | 372 +++++++++++++----- tests/extras/cassettes/test_from_hgvs.yaml | 59 ++- ...NC_000007.14:g.55181220del-expected2].yaml | 30 +- ...g.55181230_55181231insGGCT-expected3].yaml | 38 +- ...NC_000007.14:g.55181320A>T-expected1].yaml | 65 ++- ...NC_000013.11:g.32316467dup-expected5].yaml | 30 +- ....11:g.32331093_32331094dup-expected4].yaml | 78 ++-- ...s[NC_000013.11:g.32936732=-expected0].yaml | 126 +++++- ....10:g.289464_289465insCACA-expected8].yaml | 136 +++++-- ...0019.10:g.289485_289500del-expected9].yaml | 52 +-- ...vs[NM_001331029.1:n.872A>G-expected6].yaml | 26 +- ...hgvs[NM_181798.1:n.1263G>T-expected7].yaml | 94 ++++- ...[NM_001331029.1:n.872A>G-vo_as_dict6].yaml | 61 --- ...vs[NM_181798.1:n.1263G>T-vo_as_dict7].yaml | 61 --- tests/extras/cassettes/test_to_spdi.yaml | 74 ---- tests/extras/test_allele_translator.py | 34 +- 19 files changed, 941 insertions(+), 495 deletions(-) delete mode 100644 tests/extras/cassettes/test_rest_dp_to_hgvs[NM_001331029.1:n.872A>G-vo_as_dict6].yaml delete mode 100644 tests/extras/cassettes/test_rest_dp_to_hgvs[NM_181798.1:n.1263G>T-vo_as_dict7].yaml delete mode 100644 tests/extras/cassettes/test_to_spdi.yaml diff --git a/setup.cfg b/setup.cfg index def13ba1..b12ca2ea 100644 --- a/setup.cfg +++ b/setup.cfg @@ -92,7 +92,7 @@ extras = psycopg2-binary biocommons.seqrepo>=0.5.1 bioutils>=0.5.2 - hgvs>=1.4 + hgvs@git+https://github.com/biocommons/hgvs@225-uncertain-ranges requests dill~=0.3.7 click diff --git a/src/ga4gh/vrs/extras/translator.py b/src/ga4gh/vrs/extras/translator.py index f3faa987..d8b00bfc 100644 --- a/src/ga4gh/vrs/extras/translator.py +++ b/src/ga4gh/vrs/extras/translator.py @@ -46,10 +46,9 @@ class Translator: r"(?P[^-]+)-(?P\d+)-(?P[ACGTURYKMSWBDHVN]+)-(?P[ACGTURYKMSWBDHVN]+)", re.IGNORECASE ) - hgvs_re = re.compile(r"[^:]+:[cgnpr]\.") + hgvs_re = re.compile(r"[^:]+:[cgmnpr]\.") spdi_re = re.compile(r"(?P[^:]+):(?P\d+):(?P\w*):(?P\w*)") - def __init__( self, data_proxy, @@ -86,17 +85,34 @@ def _get_hgvs_refget_ac(self, sv: hgvs.sequencevariant.SequenceVariant): @staticmethod def _ir_stype(a): - """Get accession's sequence type""" - if a.startswith("refseq:NM_"): - return "n" - if a.startswith("refseq:NP_"): - return "p" - if a.startswith("refseq:NG_"): - return "g" - if a.startswith("refseq:NC_"): - return "g" - if a.startswith("GRCh"): - return "g" + """ + The purpose of this function is to provide a convenient way to extract the sequence type from an accession by matching its prefix to a known set of prefixes. + + Args: + a (str): The accession string. + + Returns: + str or None: The sequence type associated with the accession string, or None if no matching prefix is found. + """ + + prefix_dict = { + "refseq:NM_": "n", + "refseq:NC_012920": "m", + "refseq:NG_": "g", + "refseq:NC_00": "g", + "refseq:NW_": "g", + "refseq:NT_": "g", + "refseq:NR_": "n", + "refseq:NP_": "p", + "refseq:XM_": "n", + "refseq:XR_": "n", + "refseq:XP_": "p", + "GRCh": "g", + } + + for prefix, stype in prefix_dict.items(): + if a.startswith(prefix): + return stype return None def translate_from(self, var, fmt=None, **kwargs): @@ -152,7 +168,6 @@ def translate_to(self, vo, fmt): t = self.to_translators[fmt] return t(vo) - ############################################################################ # INTERNAL @@ -580,7 +595,7 @@ def _to_hgvs(self, vo, namespace="refseq"): if ns.startswith("GRC") and namespace is None: continue - if not (any(a.startswith(pfx) for pfx in ("NM", "NP", "NC", "NG"))): + if not (any(a.startswith(pfx) for pfx in ("NM", "NP", "NC", "NG", "NR", "NW", "NT", "XM", "XR", "XP"))): continue var.ac = a @@ -727,7 +742,7 @@ def _post_process_imported_cnv(self, copy_number): from ga4gh.vrs.dataproxy import create_dataproxy # dp = create_dataproxy("seqrepo+file:///usr/local/share/seqrepo/latest") - dp = create_dataproxy("seqrepo + http://localhost:5555/seqrepo") + dp = create_dataproxy("seqrepo + http://localhost:5000/seqrepo") tlr = Translator(data_proxy=dp) expressions = [ diff --git a/tests/extras/cassettes/test_from_beacon.yaml b/tests/extras/cassettes/test_from_beacon.yaml index 019b55b4..41870c8f 100644 --- a/tests/extras/cassettes/test_from_beacon.yaml +++ b/tests/extras/cassettes/test_from_beacon.yaml @@ -9,7 +9,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:19 response: @@ -35,7 +35,54 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:29:22 GMT + Server: + - Werkzeug/2.2.2 Python/3.10.4 + status: + code: 200 + message: OK +- request: + body: null + headers: + Accept: + - '*/*' + Accept-Encoding: + - gzip, deflate + Connection: + - keep-alive + User-Agent: + - python-requests/2.31.0 + method: GET + uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:MT + response: + body: + string: "{\n \"added\": \"2016-08-24T06:13:07Z\",\n \"aliases\": [\n \"Ensembl:MT\",\n + \ \"ensembl:MT\",\n \"GRCh37.p10:MT\",\n \"GRCh37.p10:chrM\",\n \"GRCh37.p11:MT\",\n + \ \"GRCh37.p11:chrM\",\n \"GRCh37.p12:MT\",\n \"GRCh37.p12:chrM\",\n + \ \"GRCh37.p13:MT\",\n \"GRCh37.p13:chrM\",\n \"GRCh37.p2:MT\",\n + \ \"GRCh37.p2:chrM\",\n \"GRCh37.p5:MT\",\n \"GRCh37.p5:chrM\",\n + \ \"GRCh37.p9:MT\",\n \"GRCh37.p9:chrM\",\n \"GRCh38:MT\",\n \"GRCh38:chrM\",\n + \ \"GRCh38.p1:MT\",\n \"GRCh38.p1:chrM\",\n \"GRCh38.p10:MT\",\n \"GRCh38.p10:chrM\",\n + \ \"GRCh38.p11:MT\",\n \"GRCh38.p11:chrM\",\n \"GRCh38.p12:MT\",\n + \ \"GRCh38.p12:chrM\",\n \"GRCh38.p2:MT\",\n \"GRCh38.p2:chrM\",\n + \ \"GRCh38.p3:MT\",\n \"GRCh38.p3:chrM\",\n \"GRCh38.p4:MT\",\n \"GRCh38.p4:chrM\",\n + \ \"GRCh38.p5:MT\",\n \"GRCh38.p5:chrM\",\n \"GRCh38.p6:MT\",\n \"GRCh38.p6:chrM\",\n + \ \"GRCh38.p7:MT\",\n \"GRCh38.p7:chrM\",\n \"GRCh38.p8:MT\",\n \"GRCh38.p8:chrM\",\n + \ \"GRCh38.p9:MT\",\n \"GRCh38.p9:chrM\",\n \"MD5:c68f52674c9fb33aef52dcf399755519\",\n + \ \"NCBI:NC_012920.1\",\n \"refseq:NC_012920.1\",\n \"SEGUID:eQNFYXnsCzhp/MkfBUBVnuFZzTA\",\n + \ \"SHA1:7903456179ec0b3869fcc91f0540559ee159cd30\",\n \"VMC:GS_k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n + \ \"sha512t24u:k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n \"ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n + \ \"hs37-1kg:MT\",\n \"hs37d5:MT\"\n ],\n \"alphabet\": \"ACGNT\",\n + \ \"length\": 16569\n}\n" + headers: + Connection: + - close + Content-Length: + - '1355' + Content-Type: + - application/json + Date: + - Wed, 13 Mar 2024 11:29:22 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: diff --git a/tests/extras/cassettes/test_from_gnomad.yaml b/tests/extras/cassettes/test_from_gnomad.yaml index bacd5104..bcd6bfbf 100644 --- a/tests/extras/cassettes/test_from_gnomad.yaml +++ b/tests/extras/cassettes/test_from_gnomad.yaml @@ -9,12 +9,59 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET - uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:19?start=44908821&end=44908822 + uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:MT response: body: - string: C + string: "{\n \"added\": \"2016-08-24T06:13:07Z\",\n \"aliases\": [\n \"Ensembl:MT\",\n + \ \"ensembl:MT\",\n \"GRCh37.p10:MT\",\n \"GRCh37.p10:chrM\",\n \"GRCh37.p11:MT\",\n + \ \"GRCh37.p11:chrM\",\n \"GRCh37.p12:MT\",\n \"GRCh37.p12:chrM\",\n + \ \"GRCh37.p13:MT\",\n \"GRCh37.p13:chrM\",\n \"GRCh37.p2:MT\",\n + \ \"GRCh37.p2:chrM\",\n \"GRCh37.p5:MT\",\n \"GRCh37.p5:chrM\",\n + \ \"GRCh37.p9:MT\",\n \"GRCh37.p9:chrM\",\n \"GRCh38:MT\",\n \"GRCh38:chrM\",\n + \ \"GRCh38.p1:MT\",\n \"GRCh38.p1:chrM\",\n \"GRCh38.p10:MT\",\n \"GRCh38.p10:chrM\",\n + \ \"GRCh38.p11:MT\",\n \"GRCh38.p11:chrM\",\n \"GRCh38.p12:MT\",\n + \ \"GRCh38.p12:chrM\",\n \"GRCh38.p2:MT\",\n \"GRCh38.p2:chrM\",\n + \ \"GRCh38.p3:MT\",\n \"GRCh38.p3:chrM\",\n \"GRCh38.p4:MT\",\n \"GRCh38.p4:chrM\",\n + \ \"GRCh38.p5:MT\",\n \"GRCh38.p5:chrM\",\n \"GRCh38.p6:MT\",\n \"GRCh38.p6:chrM\",\n + \ \"GRCh38.p7:MT\",\n \"GRCh38.p7:chrM\",\n \"GRCh38.p8:MT\",\n \"GRCh38.p8:chrM\",\n + \ \"GRCh38.p9:MT\",\n \"GRCh38.p9:chrM\",\n \"MD5:c68f52674c9fb33aef52dcf399755519\",\n + \ \"NCBI:NC_012920.1\",\n \"refseq:NC_012920.1\",\n \"SEGUID:eQNFYXnsCzhp/MkfBUBVnuFZzTA\",\n + \ \"SHA1:7903456179ec0b3869fcc91f0540559ee159cd30\",\n \"VMC:GS_k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n + \ \"sha512t24u:k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n \"ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n + \ \"hs37-1kg:MT\",\n \"hs37d5:MT\"\n ],\n \"alphabet\": \"ACGNT\",\n + \ \"length\": 16569\n}\n" + headers: + Connection: + - close + Content-Length: + - '1355' + Content-Type: + - application/json + Date: + - Wed, 13 Mar 2024 11:38:59 GMT + Server: + - Werkzeug/2.2.2 Python/3.10.4 + status: + code: 200 + message: OK +- request: + body: null + headers: + Accept: + - '*/*' + Accept-Encoding: + - gzip, deflate + Connection: + - keep-alive + User-Agent: + - python-requests/2.31.0 + method: GET + uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:MT?start=10082&end=10083 + response: + body: + string: A headers: Connection: - close @@ -23,7 +70,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -39,7 +86,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:13 response: @@ -65,7 +112,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -81,7 +128,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:13?start=20003095&end=20003097 response: @@ -95,7 +142,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -111,7 +158,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:13?start=20003009&end=20003010 response: @@ -125,7 +172,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -141,7 +188,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:13?start=19993837&end=19993839 response: @@ -155,7 +202,49 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT + Server: + - Werkzeug/2.2.2 Python/3.10.4 + status: + code: 200 + message: OK +- request: + body: null + headers: + Accept: + - '*/*' + Accept-Encoding: + - gzip, deflate + Connection: + - keep-alive + User-Agent: + - python-requests/2.31.0 + method: GET + uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:19 + response: + body: + string: "{\n \"added\": \"2016-08-24T08:19:02Z\",\n \"aliases\": [\n \"Ensembl:19\",\n + \ \"ensembl:19\",\n \"GRCh38:19\",\n \"GRCh38:chr19\",\n \"GRCh38.p1:19\",\n + \ \"GRCh38.p1:chr19\",\n \"GRCh38.p10:19\",\n \"GRCh38.p10:chr19\",\n + \ \"GRCh38.p11:19\",\n \"GRCh38.p11:chr19\",\n \"GRCh38.p12:19\",\n + \ \"GRCh38.p12:chr19\",\n \"GRCh38.p2:19\",\n \"GRCh38.p2:chr19\",\n + \ \"GRCh38.p3:19\",\n \"GRCh38.p3:chr19\",\n \"GRCh38.p4:19\",\n \"GRCh38.p4:chr19\",\n + \ \"GRCh38.p5:19\",\n \"GRCh38.p5:chr19\",\n \"GRCh38.p6:19\",\n \"GRCh38.p6:chr19\",\n + \ \"GRCh38.p7:19\",\n \"GRCh38.p7:chr19\",\n \"GRCh38.p8:19\",\n \"GRCh38.p8:chr19\",\n + \ \"GRCh38.p9:19\",\n \"GRCh38.p9:chr19\",\n \"MD5:b0eba2c7bb5c953d1e06a508b5e487de\",\n + \ \"NCBI:NC_000019.10\",\n \"refseq:NC_000019.10\",\n \"SEGUID:AHxM5/L8jIX08UhBBkKXkiO5rhY\",\n + \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n + \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n + \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" + headers: + Connection: + - close + Content-Length: + - '1035' + Content-Type: + - application/json + Date: + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -171,7 +260,37 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 + method: GET + uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:19?start=44908821&end=44908822 + response: + body: + string: C + headers: + Connection: + - close + Content-Length: + - '1' + Content-Type: + - text/plain; charset=utf-8 + Date: + - Wed, 13 Mar 2024 11:38:59 GMT + Server: + - Werkzeug/2.2.2 Python/3.10.4 + status: + code: 200 + message: OK +- request: + body: null + headers: + Accept: + - '*/*' + Accept-Encoding: + - gzip, deflate + Connection: + - keep-alive + User-Agent: + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl response: @@ -197,7 +316,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -213,7 +332,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=44908821&end=44908822 response: @@ -227,7 +346,84 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT + Server: + - Werkzeug/2.2.2 Python/3.10.4 + status: + code: 200 + message: OK +- request: + body: null + headers: + Accept: + - '*/*' + Accept-Encoding: + - gzip, deflate + Connection: + - keep-alive + User-Agent: + - python-requests/2.31.0 + method: GET + uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct + response: + body: + string: "{\n \"added\": \"2016-08-24T06:13:07Z\",\n \"aliases\": [\n \"Ensembl:MT\",\n + \ \"ensembl:MT\",\n \"GRCh37.p10:MT\",\n \"GRCh37.p10:chrM\",\n \"GRCh37.p11:MT\",\n + \ \"GRCh37.p11:chrM\",\n \"GRCh37.p12:MT\",\n \"GRCh37.p12:chrM\",\n + \ \"GRCh37.p13:MT\",\n \"GRCh37.p13:chrM\",\n \"GRCh37.p2:MT\",\n + \ \"GRCh37.p2:chrM\",\n \"GRCh37.p5:MT\",\n \"GRCh37.p5:chrM\",\n + \ \"GRCh37.p9:MT\",\n \"GRCh37.p9:chrM\",\n \"GRCh38:MT\",\n \"GRCh38:chrM\",\n + \ \"GRCh38.p1:MT\",\n \"GRCh38.p1:chrM\",\n \"GRCh38.p10:MT\",\n \"GRCh38.p10:chrM\",\n + \ \"GRCh38.p11:MT\",\n \"GRCh38.p11:chrM\",\n \"GRCh38.p12:MT\",\n + \ \"GRCh38.p12:chrM\",\n \"GRCh38.p2:MT\",\n \"GRCh38.p2:chrM\",\n + \ \"GRCh38.p3:MT\",\n \"GRCh38.p3:chrM\",\n \"GRCh38.p4:MT\",\n \"GRCh38.p4:chrM\",\n + \ \"GRCh38.p5:MT\",\n \"GRCh38.p5:chrM\",\n \"GRCh38.p6:MT\",\n \"GRCh38.p6:chrM\",\n + \ \"GRCh38.p7:MT\",\n \"GRCh38.p7:chrM\",\n \"GRCh38.p8:MT\",\n \"GRCh38.p8:chrM\",\n + \ \"GRCh38.p9:MT\",\n \"GRCh38.p9:chrM\",\n \"MD5:c68f52674c9fb33aef52dcf399755519\",\n + \ \"NCBI:NC_012920.1\",\n \"refseq:NC_012920.1\",\n \"SEGUID:eQNFYXnsCzhp/MkfBUBVnuFZzTA\",\n + \ \"SHA1:7903456179ec0b3869fcc91f0540559ee159cd30\",\n \"VMC:GS_k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n + \ \"sha512t24u:k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n \"ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n + \ \"hs37-1kg:MT\",\n \"hs37d5:MT\"\n ],\n \"alphabet\": \"ACGNT\",\n + \ \"length\": 16569\n}\n" + headers: + Connection: + - close + Content-Length: + - '1355' + Content-Type: + - application/json + Date: + - Wed, 13 Mar 2024 11:38:59 GMT + Server: + - Werkzeug/2.2.2 Python/3.10.4 + status: + code: 200 + message: OK +- request: + body: null + headers: + Accept: + - '*/*' + Accept-Encoding: + - gzip, deflate + Connection: + - keep-alive + User-Agent: + - python-requests/2.31.0 + method: GET + uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct?start=10082&end=10083 + response: + body: + string: A + headers: + Connection: + - close + Content-Length: + - '1' + Content-Type: + - text/plain; charset=utf-8 + Date: + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -243,7 +439,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT response: @@ -269,7 +465,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -285,7 +481,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003095&end=20003097 response: @@ -299,7 +495,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -315,7 +511,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003096&end=20003097 response: @@ -329,7 +525,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -345,7 +541,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003095&end=20003096 response: @@ -359,7 +555,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -375,7 +571,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003097&end=20003098 response: @@ -389,7 +585,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -405,7 +601,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003096&end=20003096 response: @@ -419,7 +615,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -435,7 +631,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003097&end=20003097 response: @@ -449,7 +645,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -465,7 +661,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003009&end=20003010 response: @@ -479,7 +675,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -495,7 +691,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003010&end=20003010 response: @@ -509,7 +705,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -525,7 +721,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003010&end=20003011 response: @@ -539,7 +735,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -555,7 +751,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993837&end=19993839 response: @@ -569,7 +765,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -585,7 +781,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993839&end=19993839 response: @@ -599,7 +795,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -615,7 +811,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993838&end=19993839 response: @@ -629,7 +825,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -645,7 +841,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993837&end=19993838 response: @@ -659,7 +855,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -675,7 +871,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993836&end=19993837 response: @@ -689,7 +885,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -705,7 +901,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993839&end=19993840 response: @@ -719,7 +915,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -735,7 +931,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:17 response: @@ -761,7 +957,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -777,7 +973,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:17?start=83129586&end=83129598 response: @@ -791,7 +987,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -807,7 +1003,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7 response: @@ -833,7 +1029,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -849,7 +1045,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129586&end=83129598 response: @@ -863,7 +1059,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -879,7 +1075,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129587&end=83129598 response: @@ -893,7 +1089,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -909,7 +1105,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129586&end=83129587 response: @@ -923,7 +1119,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -939,7 +1135,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129598&end=83129599 response: @@ -953,7 +1149,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:12 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -969,7 +1165,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129599&end=83129600 response: @@ -983,7 +1179,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -999,7 +1195,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129600&end=83129601 response: @@ -1013,7 +1209,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -1029,7 +1225,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129601&end=83129602 response: @@ -1043,7 +1239,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -1059,7 +1255,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129587&end=83129587 response: @@ -1073,7 +1269,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -1089,7 +1285,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129598&end=83129601 response: @@ -1103,7 +1299,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -1119,7 +1315,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129587&end=83129601 response: @@ -1133,7 +1329,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -1149,7 +1345,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:7 response: @@ -1174,7 +1370,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -1190,7 +1386,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:7?start=1&end=17 response: @@ -1204,7 +1400,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -1220,7 +1416,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul response: @@ -1245,7 +1441,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:38:59 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -1261,7 +1457,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=1&end=17 response: @@ -1275,7 +1471,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:39:00 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -1291,7 +1487,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=1&end=16 response: @@ -1305,7 +1501,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:39:00 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -1321,7 +1517,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:13?start=32936731&end=32936732 response: @@ -1335,7 +1531,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:39:00 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -1351,7 +1547,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32936731&end=32936732 response: @@ -1365,7 +1561,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:13 GMT + - Wed, 13 Mar 2024 11:39:00 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: diff --git a/tests/extras/cassettes/test_from_hgvs.yaml b/tests/extras/cassettes/test_from_hgvs.yaml index 227a3368..a1c65a1e 100644 --- a/tests/extras/cassettes/test_from_hgvs.yaml +++ b/tests/extras/cassettes/test_from_hgvs.yaml @@ -9,7 +9,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000019.10 response: @@ -35,7 +35,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Feb 2024 07:31:14 GMT + - Wed, 13 Mar 2024 11:29:24 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -51,7 +51,54 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 + method: GET + uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_012920.1 + response: + body: + string: "{\n \"added\": \"2016-08-24T06:13:07Z\",\n \"aliases\": [\n \"Ensembl:MT\",\n + \ \"ensembl:MT\",\n \"GRCh37.p10:MT\",\n \"GRCh37.p10:chrM\",\n \"GRCh37.p11:MT\",\n + \ \"GRCh37.p11:chrM\",\n \"GRCh37.p12:MT\",\n \"GRCh37.p12:chrM\",\n + \ \"GRCh37.p13:MT\",\n \"GRCh37.p13:chrM\",\n \"GRCh37.p2:MT\",\n + \ \"GRCh37.p2:chrM\",\n \"GRCh37.p5:MT\",\n \"GRCh37.p5:chrM\",\n + \ \"GRCh37.p9:MT\",\n \"GRCh37.p9:chrM\",\n \"GRCh38:MT\",\n \"GRCh38:chrM\",\n + \ \"GRCh38.p1:MT\",\n \"GRCh38.p1:chrM\",\n \"GRCh38.p10:MT\",\n \"GRCh38.p10:chrM\",\n + \ \"GRCh38.p11:MT\",\n \"GRCh38.p11:chrM\",\n \"GRCh38.p12:MT\",\n + \ \"GRCh38.p12:chrM\",\n \"GRCh38.p2:MT\",\n \"GRCh38.p2:chrM\",\n + \ \"GRCh38.p3:MT\",\n \"GRCh38.p3:chrM\",\n \"GRCh38.p4:MT\",\n \"GRCh38.p4:chrM\",\n + \ \"GRCh38.p5:MT\",\n \"GRCh38.p5:chrM\",\n \"GRCh38.p6:MT\",\n \"GRCh38.p6:chrM\",\n + \ \"GRCh38.p7:MT\",\n \"GRCh38.p7:chrM\",\n \"GRCh38.p8:MT\",\n \"GRCh38.p8:chrM\",\n + \ \"GRCh38.p9:MT\",\n \"GRCh38.p9:chrM\",\n \"MD5:c68f52674c9fb33aef52dcf399755519\",\n + \ \"NCBI:NC_012920.1\",\n \"refseq:NC_012920.1\",\n \"SEGUID:eQNFYXnsCzhp/MkfBUBVnuFZzTA\",\n + \ \"SHA1:7903456179ec0b3869fcc91f0540559ee159cd30\",\n \"VMC:GS_k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n + \ \"sha512t24u:k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n \"ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n + \ \"hs37-1kg:MT\",\n \"hs37d5:MT\"\n ],\n \"alphabet\": \"ACGNT\",\n + \ \"length\": 16569\n}\n" + headers: + Connection: + - 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Werkzeug/2.2.2 Python/3.10.4 status: diff --git a/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181220del-expected2].yaml b/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181220del-expected2].yaml index 9cde005a..37baf7b7 100644 --- a/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181220del-expected2].yaml +++ b/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181220del-expected2].yaml @@ -23,7 +23,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 11 Mar 2024 21:21:23 GMT + - Mon, 18 Mar 2024 19:06:47 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -53,7 +53,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 11 Mar 2024 21:21:23 GMT + - Mon, 18 Mar 2024 19:06:47 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -83,7 +83,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 11 Mar 2024 21:21:23 GMT + - Mon, 18 Mar 2024 19:06:47 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -113,7 +113,7 @@ interactions: Content-Type: - 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text/plain Date: - - Mon, 11 Mar 2024 21:21:24 GMT + - Mon, 18 Mar 2024 19:06:48 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322CFCD26EC09885000059491D137F58.1.1.m_5 + - D0BDE05998BAF2D5000030DF9C569F50.1.1.m_5 NCBI-SID: - - 11F6059A8AEDFE53_CBBESID + - CCE5AEDAB5088D90_944ESID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=11F6059A8AEDFE53_CBBESID; domain=.nih.gov; path=/; expires=Tue, 11 - Mar 2025 21:21:24 GMT + - ncbi_sid=CCE5AEDAB5088D90_944ESID; domain=.nih.gov; path=/; expires=Tue, 18 + Mar 2025 19:06:48 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: diff --git a/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181230_55181231insGGCT-expected3].yaml b/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181230_55181231insGGCT-expected3].yaml index 86e7d5a9..24b18adf 100644 --- a/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181230_55181231insGGCT-expected3].yaml +++ b/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181230_55181231insGGCT-expected3].yaml @@ -23,7 +23,7 @@ interactions: Content-Type: - 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max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -170,20 +211,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 11 Mar 2024 21:21:22 GMT + - Mon, 18 Mar 2024 19:06:47 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939BB8C393EB3495000051352B0274C2.1.1.m_5 + - D0BDE05998BAF2D5000047DF91F692FF.1.1.m_5 NCBI-SID: - - BD57D6E9DECB71A1_68D7SID + - 2410A44F14D5993A_7383SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=BD57D6E9DECB71A1_68D7SID; domain=.nih.gov; path=/; expires=Tue, 11 - Mar 2025 21:21:23 GMT + - ncbi_sid=2410A44F14D5993A_7383SID; domain=.nih.gov; path=/; expires=Tue, 18 + Mar 2025 19:06:47 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: diff --git a/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32316467dup-expected5].yaml b/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32316467dup-expected5].yaml index b6ff17d9..32b1ab08 100644 --- a/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32316467dup-expected5].yaml +++ b/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32316467dup-expected5].yaml @@ -23,7 +23,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 11 Mar 2024 21:21:31 GMT + - Mon, 18 Mar 2024 19:06:53 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -53,7 +53,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 11 Mar 2024 21:21:31 GMT + - Mon, 18 Mar 2024 19:06:53 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -83,7 +83,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 11 Mar 2024 21:21:31 GMT + - Mon, 18 Mar 2024 19:06:53 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -113,7 +113,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 11 Mar 2024 21:21:31 GMT + - Mon, 18 Mar 2024 19:06:53 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -143,7 +143,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 11 Mar 2024 21:21:31 GMT + - Mon, 18 Mar 2024 19:06:53 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -183,20 +183,20 @@ interactions: Content-Type: - text/plain Date: - 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assert tlr._from_beacon(snv_inputs["beacon"], do_normalize=False).model_dump(exclude_none=True) == snv_output + do_normalize = False + assert tlr._from_beacon(snv_inputs["beacon"], do_normalize=do_normalize).model_dump(exclude_none=True) == snv_output + assert tlr._from_beacon(mito_inputs["beacon"], do_normalize=do_normalize).model_dump(exclude_none=True) == mito_output @pytest.mark.vcr def test_from_gnomad(tlr): do_normalize = False assert tlr._from_gnomad(snv_inputs["gnomad"], do_normalize=do_normalize).model_dump(exclude_none=True) == snv_output + assert tlr._from_gnomad(mito_inputs["gnomad"], do_normalize=do_normalize).model_dump(exclude_none=True) == mito_output assert tlr._from_gnomad(deletion_inputs["gnomad"], do_normalize=do_normalize).model_dump(exclude_none=True) == gnomad_deletion_output assert tlr._from_gnomad(insertion_inputs["gnomad"], do_normalize=do_normalize).model_dump(exclude_none=True) == gnomad_insertion_output assert tlr._from_gnomad(duplication_inputs["gnomad"], do_normalize=do_normalize).model_dump(exclude_none=True) == duplication_output # do_normalize defaults to true assert tlr._from_gnomad(snv_inputs["gnomad"]).model_dump(exclude_none=True) == snv_output + assert tlr._from_gnomad(mito_inputs["gnomad"]).model_dump(exclude_none=True) == mito_output assert tlr._from_gnomad(deletion_inputs["gnomad"]).model_dump(exclude_none=True) == deletion_output_normalized assert tlr._from_gnomad(insertion_inputs["gnomad"]).model_dump(exclude_none=True) == insertion_output assert tlr._from_gnomad(duplication_inputs["gnomad"]).model_dump(exclude_none=True) == duplication_output_normalized @@ -232,6 +262,7 @@ def test_from_gnomad(tlr): def test_from_hgvs(tlr): do_normalize = False assert tlr._from_hgvs(snv_inputs["hgvs"], do_normalize=do_normalize).model_dump(exclude_none=True) == snv_output + assert tlr._from_hgvs(mito_inputs["hgvs"], do_normalize=do_normalize).model_dump(exclude_none=True) == mito_output assert tlr._from_hgvs(deletion_inputs["hgvs"], do_normalize=do_normalize).model_dump(exclude_none=True) == deletion_output assert tlr._from_hgvs(insertion_inputs["hgvs"], do_normalize=do_normalize).model_dump(exclude_none=True) == insertion_output assert tlr._from_hgvs(duplication_inputs["hgvs"], do_normalize=do_normalize).model_dump(exclude_none=True) == duplication_output @@ -241,6 +272,7 @@ def test_from_hgvs(tlr): def test_from_spdi(tlr): do_normalize = False assert tlr._from_spdi(snv_inputs["spdi"], do_normalize=do_normalize).model_dump(exclude_none=True) == snv_output + assert tlr._from_spdi(mito_inputs["spdi"], do_normalize=do_normalize).model_dump(exclude_none=True) == mito_output for spdi_del_expr in deletion_inputs["spdi"]: assert tlr._from_spdi(spdi_del_expr, do_normalize=do_normalize).model_dump(exclude_none=True) == deletion_output, spdi_del_expr for spdi_ins_expr in insertion_inputs["spdi"]: