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feat: allele rle normalization + pin pydantic version #234

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merged 16 commits into from
Aug 30, 2023
Merged

feat: allele rle normalization + pin pydantic version #234

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c8f5419
fix: allele normalization + pin pydantic version
korikuzma Aug 24, 2023
1ed754c
re-run translator tests
korikuzma Aug 24, 2023
8ac1649
didnt use new allele for state
korikuzma Aug 24, 2023
2113235
use one line
korikuzma Aug 24, 2023
b579734
include sequence in rle + paramaterize limit
korikuzma Aug 24, 2023
59424bc
maybe fixed normalize function??
korikuzma Aug 24, 2023
14e5bc9
revert
korikuzma Aug 24, 2023
6736891
fix setting trimmed alleles
korikuzma Aug 24, 2023
9938462
allow for no rle_seq_limit + update example
korikuzma Aug 24, 2023
1b7c2ff
Update src/ga4gh/vrs/normalize.py
korikuzma Aug 25, 2023
daa2195
Update src/ga4gh/vrs/normalize.py
korikuzma Aug 25, 2023
812f480
Update src/ga4gh/vrs/normalize.py
korikuzma Aug 25, 2023
af267f0
refactor handling getting alias for SequenceProxy
korikuzma Aug 30, 2023
05deaca
iri must be dereferenced + update tests
korikuzma Aug 30, 2023
b64aa8b
_normalize_allele always expects a SequenceReference
korikuzma Aug 30, 2023
2e1923a
add log warning when IRI is passed
korikuzma Aug 30, 2023
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6 changes: 5 additions & 1 deletion src/ga4gh/vrs/normalize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,10 @@ def _normalize_allele(input_allele, data_proxy, rle_seq_limit=50):
entire region of ambiguity, resulting in an unambiguous representation that may be
readily compared with other alleles.

This function assumes that IRIs are dereferenced, providing either the accession
(refseq:NC_000006.12, NC_000006.12) or ga4gh identifier for a sequence
(ga4gh:SQ.0iKlIQk2oZLoeOG9P1riRU6hvL5Ux8TV).

:param input_allele: Input VRS Allele object
:param data_proxy: SeqRepo dataproxy
:param rle_seq_limit: If RLE is set as the new state, set the limit for the length
Expand All @@ -99,7 +103,7 @@ def _normalize_allele(input_allele, data_proxy, rle_seq_limit=50):
if isinstance(allele.location.sequence, models.SequenceReference):
alias = f"ga4gh:{allele.location.sequence.refgetAccession}"
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else:
# IRI
# Dereferenced IRI
alias = allele.location.sequence.root

# Get reference sequence and interval
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56 changes: 28 additions & 28 deletions tests/cassettes/test_normalize_allele.yaml
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Expand Up @@ -11,7 +11,7 @@ interactions:
User-Agent:
- python-requests/2.31.0
method: GET
uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000006.12
uri: http://localhost:5000/seqrepo/1/metadata/NC_000006.12
response:
body:
string: "{\n \"added\": \"2016-08-27T21:22:36Z\",\n \"aliases\": [\n \"GRCh38:6\",\n
Expand All @@ -34,7 +34,7 @@ interactions:
Content-Type:
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- Wed, 30 Aug 2023 14:40:08 GMT
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Expand All @@ -52,7 +52,7 @@ interactions:
User-Agent:
- python-requests/2.31.0
method: GET
uri: http://localhost:5000/seqrepo/1/sequence/refseq:NC_000006.12?start=26090950&end=26090951
uri: http://localhost:5000/seqrepo/1/sequence/NC_000006.12?start=26090950&end=26090951
response:
body:
string: C
Expand All @@ -64,7 +64,7 @@ interactions:
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Expand Down Expand Up @@ -386,7 +386,7 @@ interactions:
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Expand All @@ -434,7 +434,7 @@ interactions:
User-Agent:
- python-requests/2.31.0
method: GET
uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000023.11
uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP
response:
body:
string: "{\n \"added\": \"2016-08-27T23:57:18Z\",\n \"aliases\": [\n \"GRCh38:X\",\n
Expand All @@ -457,7 +457,7 @@ interactions:
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4 changes: 2 additions & 2 deletions tests/test_vrs_normalize.py
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Expand Up @@ -11,7 +11,7 @@
"location": {
"end": 26090951,
"start": 26090950,
"sequence": "refseq:NC_000006.12",
"sequence": "NC_000006.12",
"type": "SequenceLocation"
},
"state": {
Expand Down Expand Up @@ -75,7 +75,7 @@
"type": "Allele",
"location": {
"type": "SequenceLocation",
"sequence": "refseq:NC_000023.11",
"sequence": "ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP",
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@ahwagner ahwagner Aug 30, 2023 •
edited
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An IRI is a reference to another object. It can be of any form under the IETF specification. When we say the sequence slot is dereferenced, it means that instead of an IRI, we have a SequenceReference object. This is true for every property in VRS where we allow for an IRI or object.

I think it is fair for us to assume this property (and every property) is dereferenced / has full object representation for normalization. We SHOULD NOT assume that an IRI takes a specific form (e.g. a refseq or ga4gh identifier) as we do here. I also believe that IRIs that contain a colon before an IRI fragment identifier (#; again, as seen here) are not valid IRIs.

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We should add a regex pattern on the IRI class. I can make a new issue for this

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An IRI is a reference to another object. It can be of any form. When we say the sequence slot is dereferenced, it means that instead of an IRI, we have a SequenceReference object. This is true for every property in VRS where we allow for an IRI or object.

Okay, I will update the code + tests to always assume a SequenceReference

We SHOULD NOT assume that an IRI takes a specific form (e.g. a refseq or ga4gh identifier) as we do here.

This was just examples for tests. The SequenceProxy class will take the input (regardless of refseq/ga4gh/ensembl etc) to get the corresponding sequence.

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When we say the sequence slot is dereferenced, it means that instead of an IRI, we have a SequenceReference object.

@ahwagner thanks for this clarification. The Translator class will need to be updated to work like this (doesn't need to be in this PR). Currently it sets the sequence id (ga4gh:SQ, not ga4gh:SQR ) as the location.sequence value

"start": [155980374, 155980375],
"end": [155980377, 155980378]
},
Expand Down