Update nullable fields, add additional fields to AlleleDescription (#680

) * Update nullable fields, add CDR fields to AlleleDescription * fix missing x-airr * Fix miairr tags in germline objects (#663). De-nest genotype (#667) * Add fwr3_end * Fix object name * Update v-sequence delineation fields and dropped aligned sequence from AlleleDescription. Updated germline test data for germline. AlleleDescription. Updated germline test data for. * Fix combined test data * Further updates to germline objects
airr-community · May 15, 2023 · 2520bbd · 2520bbd
1 parent 4e2af19
commit 2520bbd
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Showing 8 changed files with 1,439 additions and 1,037 deletions.
diff --git a/lang/R/inst/extdata/airr-schema.yaml b/lang/R/inst/extdata/airr-schema.yaml
diff --git a/lang/R/tests/data-tests/good_germline_set.json b/lang/R/tests/data-tests/good_germline_set.json
@@ -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",
@@ -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",
@@ -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",
@@ -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",