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Update nullable fields, add additional fields to AlleleDescription #680

Merged
merged 8 commits into from
May 15, 2023
Merged

Update nullable fields, add additional fields to AlleleDescription #680

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744d3db
Update nullable fields, add CDR fields to AlleleDescription
williamdlees Mar 20, 2023
267e648
fix missing x-airr
williamdlees Mar 20, 2023
e27aba2
Fix miairr tags in germline objects (#663). De-nest genotype (#667)
williamdlees Mar 30, 2023
e08d81d
Add fwr3_end
williamdlees Mar 30, 2023
8ed5aeb
Fix object name
williamdlees Mar 30, 2023
1d17eeb
Updatmne v-sequence delineation fields and dropped aligned sequence from
williamdlees Apr 8, 2023
32e3ef5
Fix combined test data
williamdlees Apr 9, 2023
46cd926
Further updates to germline objects
williamdlees May 15, 2023
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377 changes: 218 additions & 159 deletions lang/R/inst/extdata/airr-schema.yaml
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54 changes: 29 additions & 25 deletions lang/R/tests/data-tests/good_germline_set.json
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Original file line number Diff line number Diff line change
Expand Up @@ -26,16 +26,16 @@
"release_date": "24-Nov-2021",
"release_description": "First release",
"label": "IGHV-2DBF",
"sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGATGGTAGTGGCACCTACTATCTGGACTCCTTGAAGAGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA",
"coding_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGA...GGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTC............AGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA",
"sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA",
"coding_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA",
"aliases": [
"watson_et_al:CAST_EiJ_IGHV5-3"
],
"locus": "IGH",
"chromosome": null,
"sequence_type": "V",
"functional": true,
"inference_type": "Rearranged",
"inference_type": "Rearranged only",
"species": { "id": "NCBITAXON:10090", "label": "Mus musculus" },
"species_subgroup": "CAST_EiJ",
"species_subgroup_type": "strain",
Expand All @@ -57,17 +57,19 @@
{
"sequence_delineation_id": "1",
"delineation_scheme": "IMGT",
"aligned_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGA...GGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTC............AGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA",
"unaligned_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA",
"fwr1_start": 1,
"fwr1_end": 78,
"cdr1_start": 79,
"cdr1_end": 114,
"fwr2_start": 115,
"fwr2_end": 165,
"cdr2_start": 166,
"cdr2_end": 195,
"fwr3_start": 196,
"fwr3_end": 312,
"cdr3_start": 313,
"fwr1_end": 75,
"cdr1_start": 76,
"cdr1_end": 110,
"fwr2_start": 111,
"fwr2_end": 150,
"cdr2_start": 151,
"cdr2_end": 160,
"fwr3_start": 161,
"fwr3_end": 294,
"cdr3_start": 295,
"alignment": [
"1",
"2",
Expand Down Expand Up @@ -193,15 +195,15 @@
"release_description": "First release",
"label": "IGHV-2ETO",
"sequence": "CAAGTTACTCTAAAAGAGTCTGGCCCTGGGATATTGAAGCCCTCACAGACCCTCAGTCTGACTTGTTCTTTCTCTGGGTTTTCACTGAGCACTACTAATATGGGTGTAGGCTGGATTCGTCAGCCTTCAGGGAAGGGTCTGGAGTGGCTGGCACACATTTGGTGGGATGATGATAAGTACTATAACCCATCCCTGAAGAGCCGGCTAACAATCTCCAAGGATACCTCCAGAAACCAGGTATTCCTCAAGATCACCAGTGTGGACACTGCAGATACTGCCACTTACTACTGTGCTC",
"coding_sequence": "CAAGTTACTCTAAAAGAGTCTGGCCCT...GGGATATTGAAGCCCTCACAGACCCTCAGTCTGACTTGTTCTTTCTCTGGGTTTTCACTGAGC......ACTACTAATATGGGTGTAGGCTGGATTCGTCAGCCTTCAGGGAAGGGTCTGGAGTGGCTGGCACACATTTGGTGGGAT.........GATGATAAGTACTATAACCCATCCCTGAAG...AGCCGGCTAACAATCTCCAAGGATACCTCCAGAAACCAGGTATTCCTCAAGATCACCAGTGTGGACACTGCAGATACTGCCACTTACTACTGTGCTC",
"coding_sequence": "CAAGTTACTCTAAAAGAGTCTGGCCCTGGGATATTGAAGCCCTCACAGACCCTCAGTCTGACTTGTTCTTTCTCTGGGTTTTCACTGAGCACTACTAATATGGGTGTAGGCTGGATTCGTCAGCCTTCAGGGAAGGGTCTGGAGTGGCTGGCACACATTTGGTGGGATGATGATAAGTACTATAACCCATCCCTGAAGAGCCGGCTAACAATCTCCAAGGATACCTCCAGAAACCAGGTATTCCTCAAGATCACCAGTGTGGACACTGCAGATACTGCCACTTACTACTGTGCTC",
"aliases": [
"watson_et_al:CAST_EiJ_IGHV8-2"
],
"locus": "IGH",
"chromosome": null,
"sequence_type": "V",
"functional": true,
"inference_type": "Rearranged",
"inference_type": "Rearranged only",
"species": { "id": "NCBITAXON:10090", "label": "Mus musculus" },
"species_subgroup": "CAST_EiJ",
"species_subgroup_type": "strain",
Expand All @@ -223,17 +225,19 @@
{
"sequence_delineation_id": "1",
"delineation_scheme": "IMGT",
"aligned_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGA...GGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTC............AGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA",
"unaligned_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA",
"fwr1_start": 1,
"fwr1_end": 78,
"cdr1_start": 79,
"cdr1_end": 114,
"fwr2_start": 115,
"fwr2_end": 165,
"cdr2_start": 166,
"cdr2_end": 195,
"fwr3_start": 196,
"fwr3_end": 312,
"cdr3_start": 313,
"fwr1_end": 75,
"cdr1_start": 76,
"cdr1_end": 110,
"fwr2_start": 111,
"fwr2_end": 150,
"cdr2_start": 151,
"cdr2_end": 160,
"fwr3_start": 161,
"fwr3_end": 294,
"cdr3_start": 295,
"alignment": [
"1",
"2",
Expand Down
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