From 30f436f75c57b5cd08ad4921678cdea45ee5435f Mon Sep 17 00:00:00 2001 From: Christian Busse Date: Wed, 21 Feb 2024 13:33:06 +0100 Subject: [PATCH] Troubleshot combined YAML --- .../python/tests/data/good_combined_airr.yaml | 876 +++++++++--------- 1 file changed, 438 insertions(+), 438 deletions(-) diff --git a/lang/python/tests/data/good_combined_airr.yaml b/lang/python/tests/data/good_combined_airr.yaml index 5dcbc82f3..7b9fb4390 100644 --- a/lang/python/tests/data/good_combined_airr.yaml +++ b/lang/python/tests/data/good_combined_airr.yaml @@ -89,40 +89,40 @@ Repertoire: immunogen: intervention: medical_history: - genotype: - receptor_genotype_set: - receptor_genotype_set_id: '1' - genotype_class_list: - - receptor_genotype_id: '1' - locus: IGH - documented_alleles: - - label: IGHV1-69*01 - germline_set_ref: IMGT:Homo sapiens:2022.1.31 - phasing: 1 - - label: IGHV1-69*02 - germline_set_ref: IMGT:Homo sapiens:2022.1.31 - phasing: 2 - undocumented_alleles: - - allele_name: IGHD3-1*01_S1234 - sequence: agtagtagtagt - phasing: 1 - deleted_genes: - - label: IGHV3-30-3 - germline_set_ref: IMGT:Homo sapiens:2022.1.31 - phasing: 1 - inference_process: repertoire_sequencing - mhc_genotype_set: - mhc_genotype_set_id: "this is a unique identifier" - mhc_genotype_list: - - mhc_genotype_id: unique - mhc_class: MHC-I - mhc_genotyping_method: pcr_low_resolution - mhc_alleles: - - allele_designation: "01:01" - gene: - id: "MRO-0000046" - label: "HLA-A" - reference_set_ref: blah + # genotype: + # receptor_genotype_set: + # receptor_genotype_set_id: '1' + # genotype_class_list: + # - receptor_genotype_id: '1' + # locus: IGH + # documented_alleles: + # - label: IGHV1-69*01 + # germline_set_ref: IMGT:Homo sapiens:2022.1.31 + # phasing: 1 + # - label: IGHV1-69*02 + # germline_set_ref: IMGT:Homo sapiens:2022.1.31 + # phasing: 2 + # undocumented_alleles: + # - allele_name: IGHD3-1*01_S1234 + # sequence: agtagtagtagt + # phasing: 1 + # deleted_genes: + # - label: IGHV3-30-3 + # germline_set_ref: IMGT:Homo sapiens:2022.1.31 + # phasing: 1 + # inference_process: repertoire_sequencing + # mhc_genotype_set: + # mhc_genotype_set_id: "this is a unique identifier" + # mhc_genotype_list: + # - mhc_genotype_id: unique + # mhc_class: MHC-I + # mhc_genotyping_method: pcr_low_resolution + # mhc_alleles: + # - allele_designation: "01:01" + # gene: + # id: "MRO-0000046" + # label: "HLA-A" + # reference_set_ref: blah sample: - sample_id: TW01A_B_naive sample_processing_id: @@ -529,407 +529,407 @@ Repertoire: germline_database: analysis_provenance_id: 4625424004665971176-242ac11c-0001-012 -GermlineSet: -- acknowledgements: - - contributor_id: "3" - name: "William Lees" - orcid_id: - - id: "ORCID:0000-0001-9834-6840" - label: "William Lees" - affiliation: - - id: "ROR:02mb95055" - label: "Birkbeck, University of London" - affiliation_department: null - contributions: - - role: "investigation" - degree: null - - role: "data curation" - degree: null - allele_descriptions: - - acknowledgements: - - contributor_id: "3" - name: "William Lees" - orcid_id: - - id: "ORCID:0000-0001-9834-6840" - label: "William Lees" - affiliation: - - id: "ROR:02mb95055" - label: "Birkbeck, University of London" - affiliation_department: null - contributions: - - role: "investigation" - degree: null - - role: "data curation" - degree: null - aliases: - - watson_et_al:CAST_EiJ_IGHV5-3 - allele_description_id: OGRDB:A00301 - allele_description_ref: OGRDB:Mouse_IGH:IGHV-2DBF - allele_designation: null - chromosome: null - coding_sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA - curation: 'Imported to OGRDB with the following notes: watson_et_al: CAST_EiJ_IGHV5-3' - curational_tags: null - functional: true - gene_designation: null - gene_end: null - gene_start: null - inference_type: rearranged_only - label: IGHV-2DBF - leader_1_end: null - leader_1_start: null - leader_2_end: null - leader_2_start: null - locus: IGH - paralogs: [] - rearranged_support: [] - release_date: 2021-11-24 - release_description: First release - release_version: 1 - sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA - sequence_type: V - species: - id: NCBITAXON:10090 - label: Mus musculus - species_subgroup: CAST_EiJ - species_subgroup_type: strain - status: active - subgroup_designation: null - unrearranged_support: [] - utr_5_prime_end: null - utr_5_prime_start: null - v_gene_delineations: - - aligned_sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGA...GGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTC............AGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA - alignment: - - '1' - - '2' - - '3' - - '4' - - '5' - - '6' - - '7' - - '8' - - '9' - - '10' - - '11' - - '12' - - '13' - - '14' - - '15' - - '16' - - '17' - - '18' - - '19' - - '20' - - '21' - - '22' - - '23' - - '24' - - '25' - - '26' - - '27' - - '28' - - '29' - - '30' - - '31' - - '32' - - '33' - - '34' - - '35' - - '36' - - '37' - - '38' - - '39' - - '40' - - '41' - - '42' - - '43' - - '44' - - '45' - - '46' - - '47' - - '48' - - '49' - - '50' - - '51' - - '52' - - '53' - - '54' - - '55' - - '56' - - '57' - - '58' - - '59' - - '60' - - '61' - - '62' - - '63' - - '64' - - '65' - - '66' - - '67' - - '68' - - '69' - - '70' - - '71' - - '72' - - '73' - - '74' - - '75' - - '76' - - '77' - - '78' - - '79' - - '80' - - '81' - - '82' - - '83' - - '84' - - '85' - - '86' - - '87' - - '88' - - '89' - - '90' - - '91' - - '92' - - '93' - - '94' - - '95' - - '96' - - '97' - - '98' - - '99' - - '100' - - '101' - - '102' - - '103' - - '104' - cdr1_end: 110 - cdr1_start: 76 - cdr2_end: 160 - cdr2_start: 151 - cdr3_start: 295 - delineation_scheme: IMGT - fwr1_end: 75 - fwr1_start: 1 - fwr2_end: 150 - fwr2_start: 111 - fwr3_end: 294 - fwr3_start: 161 - sequence_delineation_id: '1' - unaligned_sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA - v_rs_end: null - v_rs_start: null - - acknowledgements: - - contributor_id: "3" - name: "William Lees" - orcid_id: - - id: "ORCID:0000-0001-9834-6840" - label: "William Lees" - affiliation: - - id: "ROR:02mb95055" - label: "Birkbeck, University of London" - affiliation_department: null - contributions: - - role: "investigation" - degree: null - - role: "data curation" - degree: null - aliases: - - watson_et_al:CAST_EiJ_IGHV8-2 - allele_description_id: OGRDB:A00314 - allele_description_ref: OGRDB:Mouse_IGH:IGHV-2ETO - allele_designation: null - chromosome: null - coding_sequence: CAAGTTACTCTAAAAGAGTCTGGCCCTGGGATATTGAAGCCCTCACAGACCCTCAGTCTGACTTGTTCTTTCTCTGGGTTTTCACTGAGCACTACTAATATGGGTGTAGGCTGGATTCGTCAGCCTTCAGGGAAGGGTCTGGAGTGGCTGGCACACATTTGGTGGGATGATGATAAGTACTATAACCCATCCCTGAAGAGCCGGCTAACAATCTCCAAGGATACCTCCAGAAACCAGGTATTCCTCAAGATCACCAGTGTGGACACTGCAGATACTGCCACTTACTACTGTGCTC - curation: 'Imported to OGRDB with the following notes: watson_et_al: CAST_EiJ_IGHV8-2' - curational_tags: null - functional: true - gene_designation: null - gene_end: null - gene_start: null - inference_type: rearranged_only - label: IGHV-2ETO - leader_1_end: null - leader_1_start: null - leader_2_end: null - leader_2_start: null - locus: IGH - paralogs: [] - rearranged_support: [] - release_date: 2021-11-24 - release_description: First release - release_version: 1 - sequence: CAAGTTACTCTAAAAGAGTCTGGCCCTGGGATATTGAAGCCCTCACAGACCCTCAGTCTGACTTGTTCTTTCTCTGGGTTTTCACTGAGCACTACTAATATGGGTGTAGGCTGGATTCGTCAGCCTTCAGGGAAGGGTCTGGAGTGGCTGGCACACATTTGGTGGGATGATGATAAGTACTATAACCCATCCCTGAAGAGCCGGCTAACAATCTCCAAGGATACCTCCAGAAACCAGGTATTCCTCAAGATCACCAGTGTGGACACTGCAGATACTGCCACTTACTACTGTGCTC - sequence_type: V - species: - id: NCBITAXON:10090 - label: Mus musculus - species_subgroup: CAST_EiJ - species_subgroup_type: strain - status: active - subgroup_designation: null - unrearranged_support: [] - utr_5_prime_end: null - utr_5_prime_start: null - v_gene_delineations: - - aligned_sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGA...GGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTC............AGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA - alignment: - - '1' - - '2' - - '3' - - '4' - - '5' - - '6' - - '7' - - '8' - - '9' - - '10' - - '11' - - '12' - - '13' - - '14' - - '15' - - '16' - - '17' - - '18' - - '19' - - '20' - - '21' - - '22' - - '23' - - '24' - - '25' - - '26' - - '27' - - '28' - - '29' - - '30' - - '31' - - '32' - - '33' - - '34' - - '35' - - '36' - - '37' - - '38' - - '39' - - '40' - - '41' - - '42' - - '43' - - '44' - - '45' - - '46' - - '47' - - '48' - - '49' - - '50' - - '51' - - '52' - - '53' - - '54' - - '55' - - '56' - - '57' - - '58' - - '59' - - '60' - - '61' - - '62' - - '63' - - '64' - - '65' - - '66' - - '67' - - '68' - - '69' - - '70' - - '71' - - '72' - - '73' - - '74' - - '75' - - '76' - - '77' - - '78' - - '79' - - '80' - - '81' - - '82' - - '83' - - '84' - - '85' - - '86' - - '87' - - '88' - - '89' - - '90' - - '91' - - '92' - - '93' - - '94' - - '95' - - '96' - - '97' - - '98' - - '99' - - '100' - - '101' - - '102' - - '103' - - '104' - cdr1_end: 110 - cdr1_start: 76 - cdr2_end: 160 - cdr2_start: 151 - cdr3_start: 295 - delineation_scheme: IMGT - fwr1_end: 75 - fwr1_start: 1 - fwr2_end: 150 - fwr2_start: 111 - fwr3_end: 294 - fwr3_start: 161 - sequence_delineation_id: '1' - unaligned_sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA - v_rs_end: null - v_rs_start: null - curation: null - germline_set_id: OGRDB:G00007 - germline_set_name: CAST IGH - germline_set_ref: OGRDB:G00007.1 - locus: IGH - pub_ids: [''] - release_date: '2021-11-24' - release_description: '' - release_version: 1 - species: - id: NCBITAXON:10090 - label: Mus musculus - species_subgroup: CAST_EiJ - species_subgroup_type: strain - - -GenotypeSet: - - receptor_genotype_set_id: '1' - genotype_class_list: - - receptor_genotype_id: '1' - locus: IGH - documented_alleles: - - label: IGHV1-69*01 - germline_set_ref: IMGT:Homo sapiens:2022.1.31 - phasing: 1 - - label: IGHV1-69*02 - germline_set_ref: IMGT:Homo sapiens:2022.1.31 - phasing: 2 - undocumented_alleles: - - allele_name: IGHD3-1*01_S1234 - sequence: agtagtagtagt - phasing: 1 - deleted_genes: - - label: IGHV3-30-3 - germline_set_ref: IMGT:Homo sapiens:2022.1.31 - phasing: 1 - inference_process: repertoire_sequencing +# GermlineSet: +# - acknowledgements: +# - contributor_id: "3" +# name: "William Lees" +# orcid_id: +# - id: "ORCID:0000-0001-9834-6840" +# label: "William Lees" +# affiliation: +# - id: "ROR:02mb95055" +# label: "Birkbeck, University of London" +# affiliation_department: null +# contributions: +# - role: "investigation" +# degree: null +# - role: "data curation" +# degree: null +# allele_descriptions: +# - acknowledgements: +# - contributor_id: "3" +# name: "William Lees" +# orcid_id: +# - id: "ORCID:0000-0001-9834-6840" +# label: "William Lees" +# affiliation: +# - id: "ROR:02mb95055" +# label: "Birkbeck, University of London" +# affiliation_department: null +# contributions: +# - role: "investigation" +# degree: null +# - role: "data curation" +# degree: null +# aliases: +# - watson_et_al:CAST_EiJ_IGHV5-3 +# allele_description_id: OGRDB:A00301 +# allele_description_ref: OGRDB:Mouse_IGH:IGHV-2DBF +# allele_designation: null +# chromosome: null +# coding_sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA +# curation: 'Imported to OGRDB with the following notes: watson_et_al: CAST_EiJ_IGHV5-3' +# curational_tags: null +# functional: true +# gene_designation: null +# gene_end: null +# gene_start: null +# inference_type: rearranged_only +# label: IGHV-2DBF +# leader_1_end: null +# leader_1_start: null +# leader_2_end: null +# leader_2_start: null +# locus: IGH +# paralogs: [] +# rearranged_support: [] +# release_date: 2021-11-24 +# release_description: First release +# release_version: 1 +# sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA +# sequence_type: V +# species: +# id: NCBITAXON:10090 +# label: Mus musculus +# species_subgroup: CAST_EiJ +# species_subgroup_type: strain +# status: active +# subgroup_designation: null +# unrearranged_support: [] +# utr_5_prime_end: null +# utr_5_prime_start: null +# v_gene_delineations: +# - aligned_sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGA...GGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTC............AGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA +# alignment: +# - '1' +# - '2' +# - '3' +# - '4' +# - '5' +# - '6' +# - '7' +# - '8' +# - '9' +# - '10' +# - '11' +# - '12' +# - '13' +# - '14' +# - '15' +# - '16' +# - '17' +# - '18' +# - '19' +# - '20' +# - '21' +# - '22' +# - '23' +# - '24' +# - '25' +# - '26' +# - '27' +# - '28' +# - '29' +# - '30' +# - '31' +# - '32' +# - '33' +# - '34' +# - '35' +# - '36' +# - '37' +# - '38' +# - '39' +# - '40' +# - '41' +# - '42' +# - '43' +# - '44' +# - '45' +# - '46' +# - '47' +# - '48' +# - '49' +# - '50' +# - '51' +# - '52' +# - '53' +# - '54' +# - '55' +# - '56' +# - '57' +# - '58' +# - '59' +# - '60' +# - '61' +# - '62' +# - '63' +# - '64' +# - '65' +# - '66' +# - '67' +# - '68' +# - '69' +# - '70' +# - '71' +# - '72' +# - '73' +# - '74' +# - '75' +# - '76' +# - '77' +# - '78' +# - '79' +# - '80' +# - '81' +# - '82' +# - '83' +# - '84' +# - '85' +# - '86' +# - '87' +# - '88' +# - '89' +# - '90' +# - '91' +# - '92' +# - '93' +# - '94' +# - '95' +# - '96' +# - '97' +# - '98' +# - '99' +# - '100' +# - '101' +# - '102' +# - '103' +# - '104' +# cdr1_end: 110 +# cdr1_start: 76 +# cdr2_end: 160 +# cdr2_start: 151 +# cdr3_start: 295 +# delineation_scheme: IMGT +# fwr1_end: 75 +# fwr1_start: 1 +# fwr2_end: 150 +# fwr2_start: 111 +# fwr3_end: 294 +# fwr3_start: 161 +# sequence_delineation_id: '1' +# unaligned_sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA +# v_rs_end: null +# v_rs_start: null +# - acknowledgements: +# - contributor_id: "3" +# name: "William Lees" +# orcid_id: +# - id: "ORCID:0000-0001-9834-6840" +# label: "William Lees" +# affiliation: +# - id: "ROR:02mb95055" +# label: "Birkbeck, University of London" +# affiliation_department: null +# contributions: +# - role: "investigation" +# degree: null +# - role: "data curation" +# degree: null +# aliases: +# - watson_et_al:CAST_EiJ_IGHV8-2 +# allele_description_id: OGRDB:A00314 +# allele_description_ref: OGRDB:Mouse_IGH:IGHV-2ETO +# allele_designation: null +# chromosome: null +# coding_sequence: CAAGTTACTCTAAAAGAGTCTGGCCCTGGGATATTGAAGCCCTCACAGACCCTCAGTCTGACTTGTTCTTTCTCTGGGTTTTCACTGAGCACTACTAATATGGGTGTAGGCTGGATTCGTCAGCCTTCAGGGAAGGGTCTGGAGTGGCTGGCACACATTTGGTGGGATGATGATAAGTACTATAACCCATCCCTGAAGAGCCGGCTAACAATCTCCAAGGATACCTCCAGAAACCAGGTATTCCTCAAGATCACCAGTGTGGACACTGCAGATACTGCCACTTACTACTGTGCTC +# curation: 'Imported to OGRDB with the following notes: watson_et_al: CAST_EiJ_IGHV8-2' +# curational_tags: null +# functional: true +# gene_designation: null +# gene_end: null +# gene_start: null +# inference_type: rearranged_only +# label: IGHV-2ETO +# leader_1_end: null +# leader_1_start: null +# leader_2_end: null +# leader_2_start: null +# locus: IGH +# paralogs: [] +# rearranged_support: [] +# release_date: 2021-11-24 +# release_description: First release +# release_version: 1 +# sequence: CAAGTTACTCTAAAAGAGTCTGGCCCTGGGATATTGAAGCCCTCACAGACCCTCAGTCTGACTTGTTCTTTCTCTGGGTTTTCACTGAGCACTACTAATATGGGTGTAGGCTGGATTCGTCAGCCTTCAGGGAAGGGTCTGGAGTGGCTGGCACACATTTGGTGGGATGATGATAAGTACTATAACCCATCCCTGAAGAGCCGGCTAACAATCTCCAAGGATACCTCCAGAAACCAGGTATTCCTCAAGATCACCAGTGTGGACACTGCAGATACTGCCACTTACTACTGTGCTC +# sequence_type: V +# species: +# id: NCBITAXON:10090 +# label: Mus musculus +# species_subgroup: CAST_EiJ +# species_subgroup_type: strain +# status: active +# subgroup_designation: null +# unrearranged_support: [] +# utr_5_prime_end: null +# utr_5_prime_start: null +# v_gene_delineations: +# - aligned_sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGA...GGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTC............AGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA +# alignment: +# - '1' +# - '2' +# - '3' +# - '4' +# - '5' +# - '6' +# - '7' +# - '8' +# - '9' +# - '10' +# - '11' +# - '12' +# - '13' +# - '14' +# - '15' +# - '16' +# - '17' +# - '18' +# - '19' +# - '20' +# - '21' +# - '22' +# - '23' +# - '24' +# - '25' +# - '26' +# - '27' +# - '28' +# - '29' +# - '30' +# - '31' +# - '32' +# - '33' +# - '34' +# - '35' +# - '36' +# - '37' +# - '38' +# - '39' +# - '40' +# - '41' +# - '42' +# - '43' +# - '44' +# - '45' +# - '46' +# - '47' +# - '48' +# - '49' +# - '50' +# - '51' +# - '52' +# - '53' +# - '54' +# - '55' +# - '56' +# - '57' +# - '58' +# - '59' +# - '60' +# - '61' +# - '62' +# - '63' +# - '64' +# - '65' +# - '66' +# - '67' +# - '68' +# - '69' +# - '70' +# - '71' +# - '72' +# - '73' +# - '74' +# - '75' +# - '76' +# - '77' +# - '78' +# - '79' +# - '80' +# - '81' +# - '82' +# - '83' +# - '84' +# - '85' +# - '86' +# - '87' +# - '88' +# - '89' +# - '90' +# - '91' +# - '92' +# - '93' +# - '94' +# - '95' +# - '96' +# - '97' +# - '98' +# - '99' +# - '100' +# - '101' +# - '102' +# - '103' +# - '104' +# cdr1_end: 110 +# cdr1_start: 76 +# cdr2_end: 160 +# cdr2_start: 151 +# cdr3_start: 295 +# delineation_scheme: IMGT +# fwr1_end: 75 +# fwr1_start: 1 +# fwr2_end: 150 +# fwr2_start: 111 +# fwr3_end: 294 +# fwr3_start: 161 +# sequence_delineation_id: '1' +# unaligned_sequence: GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA +# v_rs_end: null +# v_rs_start: null +# curation: null +# germline_set_id: OGRDB:G00007 +# germline_set_name: CAST IGH +# germline_set_ref: OGRDB:G00007.1 +# locus: IGH +# pub_ids: [''] +# release_date: '2021-11-24' +# release_description: '' +# release_version: 1 +# species: +# id: NCBITAXON:10090 +# label: Mus musculus +# species_subgroup: CAST_EiJ +# species_subgroup_type: strain +# +# +# GenotypeSet: +# - receptor_genotype_set_id: '1' +# genotype_class_list: +# - receptor_genotype_id: '1' +# locus: IGH +# documented_alleles: +# - label: IGHV1-69*01 +# germline_set_ref: IMGT:Homo sapiens:2022.1.31 +# phasing: 1 +# - label: IGHV1-69*02 +# germline_set_ref: IMGT:Homo sapiens:2022.1.31 +# phasing: 2 +# undocumented_alleles: +# - allele_name: IGHD3-1*01_S1234 +# sequence: agtagtagtagt +# phasing: 1 +# deleted_genes: +# - label: IGHV3-30-3 +# germline_set_ref: IMGT:Homo sapiens:2022.1.31 +# phasing: 1 +# inference_process: repertoire_sequencing