partis-bcr 1.0.9.post1.dev4__cp312-cp312-manylinux1_x86_64.whl → 1.0.10.post1.dev1__cp312-cp312-manylinux1_x86_64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (45) hide show
  1. bin/parse-output.py +2 -2
  2. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/parse-output.py +2 -2
  3. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/RECORD +45 -45
  5. test/new-results/test.log +3 -3
  6. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  9. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +2 -2
  10. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  11. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  25. test/paired/new-results/run-times.csv +5 -5
  26. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +5 -5
  27. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +10 -10
  28. test/paired/new-results/subset-partition-new-simu/merged-partition.log +7 -7
  29. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  30. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  31. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  32. test/paired/new-results/test.log +50 -50
  33. test/phylo-naive-run.py +1 -1
  34. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  35. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  36. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  37. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  38. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/gctree-run.py +0 -0
  39. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  40. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/partis-test.py +0 -0
  41. {partis_bcr-1.0.9.post1.dev4.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/split-loci.py +0 -0
  42. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/WHEEL +0 -0
  43. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/entry_points.txt +0 -0
  44. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/licenses/COPYING +0 -0
  45. {partis_bcr-1.0.9.post1.dev4.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/top_level.txt +0 -0
test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml CHANGED
@@ -1 +1 @@
1
- {"version-info": {"partis-yaml": 0.1, "partis-git": {"commit": "155f2bebb9109b5cd325f7a7a89e222d7ef37b81", "tag": "v1.0.9", "n_ahead_of_tag": "4"}}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ2*01": "TGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ4*01": "TTTTGTATTTGGTGGAGGAACCCAGCTGATCATTTTAG", "IGLJ5*01": "CTGGGTGTTTGGTGAGGGGACCGAGCTGACCGTCCTAG", "IGLJ5*02": "CTGGGTGTTTGGTGAGGGGACGGAGCTGACCGTCCTAG", "IGLJ6*01": "TAATGTGTTCGGCAGTGGCACCAAGGTGACCGTCCTCG", "IGLJ7*01": "TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGTCCTCG", "IGLJ7*02": "TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGCCCTCG"}}, "cyst-positions": {"IGLV2-14*04": 267, "IGLV2-23*02": 267, "IGLV1-40*01": 267}, "phen-positions": {"IGLJ5*02": 7, "IGLJ5*01": 7, "IGLJ6*01": 7, "IGLJ7*01": 7, "IGLJ7*02": 7, "IGLJ1*01": 7, "IGLJ2*01": 7, "IGLJ4*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": 0.0, "n_clusters": 21, "n_procs": 1, "partition": [["253ca59333-igl"], ["b739ce37b7-igl"], ["aa25e6c0ce-igl"], ["7588f09c07-igl"], ["8807c8ff04-igl"], ["20909c3943-igl"], ["a3baa83300-igl"], ["971ac047ee-igl"], ["a2238f4e9a-igl"], ["8d79fca804-igl"], ["0eb272ee70-igl"], ["09f5010bd3-igl"], ["b02ee7754a-igl"], ["ddcf0ca433-igl"], ["eee6809ad6-igl"], ["14195e4958-igl"], ["d5ddf0c2ec-igl"], ["57537e5f22-igl"], ["b1e56e40a1-igl"], ["21cea6e4d0-igl"], ["4d37fe487e-igl"]]}], "events": [{"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["253ca59333-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.014970059880239521], "n_mutations": [5], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["253ca59333-igh", "b739ce37b7-igh", "b739ce37b7-igl"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1445, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["b739ce37b7-igl"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["253ca59333-igh", "253ca59333-igl", "b739ce37b7-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 297}, "k_v": {"best": 288, "min": 285, "max": 289}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-23*02": {"score": 1440, "glbounds": [0, 288], "qrbounds": [0, 288]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [288, 288]}}, "j": {"IGLJ1*01": {"score": 190, "glbounds": [0, 38], "qrbounds": [290, 328]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["aa25e6c0ce-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.029940119760479042], "n_mutations": [10], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTCGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGAACCTCCGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTGCTGCCAGTCCTTTGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["aa25e6c0ce-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1395, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["7588f09c07-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCACAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTAATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["7588f09c07-igh", "cb8a759f1a-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["8807c8ff04-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": 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["CAGTCTGCCCTG...ACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "unique_ids": ["eee6809ad6-igl"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [true], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["bc11af4843-igh", "bc11af4843-igk", "eee6809ad6-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 297}, "k_v": {"best": 288, "min": 285, "max": 289}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-23*02": {"score": 1440, "glbounds": [0, 288], "qrbounds": [0, 288]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [288, 288]}}, "j": {"IGLJ1*01": {"score": 190, "glbounds": [0, 38], "qrbounds": [290, 328]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCA........GCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "unique_ids": ["14195e4958-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [true], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [true], "paired-uids": [["14195e4958-igh", "d5ddf0c2ec-igl"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["d5ddf0c2ec-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCGGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["14195e4958-igh", "14195e4958-igl"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["57537e5f22-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["57537e5f22-igh", "7ba384a461-igh", "7ba384a461-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["b1e56e40a1-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["b1e56e40a1-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["21cea6e4d0-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["21cea6e4d0-igh", "f094dfd68a-igh", "f094dfd68a-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["4d37fe487e-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.03293413173652695], "n_mutations": [11], "input_seqs": ["TAGTCTGTGCAGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTAGGAGCAGCTCCAACATCGGTGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCATGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGCTGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["4d37fe487e-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1385, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}]}
test/paired/new-results/test.log CHANGED
@@ -21,18 +21,18 @@ smith-waterman (writing parameters)
21
21
  kept 25 (0.446) unproductive
22
22
  writing sw results to test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
23
23
  writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (0.6 sec)
24
- water time: 0.7 (ig-sw 0.6 processing 0.0)
24
+ water time: 0.7 (ig-sw 0.7 processing 0.0)
25
25
  writing hmms removed 16 genes from glfo (leaving v 6 d 18 j 4)
26
- (0.5 sec)
26
+ (0.6 sec)
27
27
  hmm
28
28
  reading output
29
29
  read 56 hmm output lines with 56 sequences in 56 events (0 failures)
30
30
  writing parameters to test/paired/new-results/test/parameters/simu/igh/hmm (0.5 sec)
31
- writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.4 sec)
31
+ writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.5 sec)
32
32
  infra time: 1.1
33
33
  hmm step time: 2.2
34
34
  writing hmms removed 3 genes from glfo (leaving v 6 d 15 j 4)
35
- (0.4 sec)
35
+ (0.3 sec)
36
36
  total time: 4.0
37
37
  cache-parameters igk:
38
38
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -63,9 +63,9 @@ smith-waterman (writing parameters)
63
63
  hmm
64
64
  reading output
65
65
  read 36 hmm output lines with 36 sequences in 36 events (0 failures)
66
- writing parameters to test/paired/new-results/test/parameters/simu/igk/hmm (0.5 sec)
67
- writing parameters to test/paired/new-results/test/parameters/simu/igk/true (0.5 sec)
68
- infra time: 1.0
66
+ writing parameters to test/paired/new-results/test/parameters/simu/igk/hmm (0.4 sec)
67
+ writing parameters to test/paired/new-results/test/parameters/simu/igk/true (0.4 sec)
68
+ infra time: 0.9
69
69
  hmm step time: 1.4
70
70
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
71
71
  (0.4 sec)
@@ -91,7 +91,7 @@ smith-waterman (writing parameters)
91
91
  kept 14 (0.667) unproductive
92
92
  writing sw results to test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml
93
93
  writing parameters to test/paired/new-results/test/parameters/simu/igl/sw (0.3 sec)
94
- water time: 0.4 (ig-sw 0.4 processing 0.0)
94
+ water time: 0.4 (ig-sw 0.3 processing 0.0)
95
95
  writing hmms removed 7 genes from glfo (leaving v 3 d 1 j 2)
96
96
  (0.1 sec)
97
97
  hmm
@@ -104,7 +104,7 @@ hmm
104
104
  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
105
105
  (0.1 sec)
106
106
  total time: 1.7
107
- total time: 12.3
107
+ total time: 12.4
108
108
  partition-new-simu partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu
109
109
  warning ignoring --plot-annotation-performance for paired clustering since it's going to be a bit fiddly to implement
110
110
  partition igh:
@@ -122,9 +122,9 @@ smith-waterman
122
122
  (0.0 sec)
123
123
  water time: 0.1
124
124
  hmm
125
- caching all 56 naive sequences (1.0s)
125
+ caching all 56 naive sequences (1.1s)
126
126
  collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
127
- 50 clusters with 10 procs (0.5s)
127
+ 50 clusters with 10 procs (0.6s)
128
128
  44 clusters with 7 procs (0.5s)
129
129
  36 clusters with 5 procs (0.4s)
130
130
  31 clusters with 3 procs (0.3s)
@@ -137,8 +137,8 @@ getting annotations for final partition
137
137
  warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: db63559ea9-igh
138
138
  (0.0 sec)
139
139
 
140
- subcluster annotation time 0.9
141
- total time: 4.9
140
+ subcluster annotation time 1.0
141
+ total time: 5.0
142
142
  partition igk:
143
143
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
144
144
  run partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igk --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/ref-results/test/simu/igk.yaml --outfname test/paired/new-results/partition-new-simu/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -164,7 +164,7 @@ hmm
164
164
  getting annotations for final partition
165
165
  subcluster annotating 6 clusters with steps: (0.3s) (0.1s) (0.1s) plotting performance (0.0 sec)
166
166
 
167
- subcluster annotation time 0.4
167
+ subcluster annotation time 0.5
168
168
  total time: 1.5
169
169
  partition igl:
170
170
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -187,7 +187,7 @@ hmm
187
187
  3 clusters with 1 proc (0.1s)
188
188
  partition loop time: 0.2
189
189
  getting annotations for final partition
190
- subcluster annotating 3 clusters with steps: (0.1s) (0.1s) (0.1s) plotting performance (0.0 sec)
190
+ subcluster annotating 3 clusters with steps: (0.2s) (0.1s) (0.1s) plotting performance (0.0 sec)
191
191
 
192
192
  subcluster annotation time 0.3
193
193
  total time: 0.9
@@ -331,7 +331,7 @@ hmm
331
331
  h 20 --> 23 +3
332
332
  k 6 --> 15 +9
333
333
  l 3 --> 8 +5
334
- total time: 19.9
334
+ total time: 20.9
335
335
  subset-partition-new-simu partis subset-partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --n-subsets 2 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu
336
336
  note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
337
337
  --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -362,7 +362,7 @@ hmm
362
362
  merging parameters from 2 subdirs (e.g. test/paired/new-results/subset-partition-new-simu/isub-0) to test/paired/new-results/subset-partition-new-simu/merged-subsets
363
363
  run partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu --input-metafnames test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/merged-subsets --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile
364
364
  log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
365
- total time: 69.3
365
+ total time: 71.1
366
366
  seed-partition-new-simu partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --max-ccf-fail-frac 0.10 --is-simu --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk --seed-loci igh:igk --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/seed-partition-new-simu
367
367
  removing seqs very different from seed seq
368
368
  wrong/no removed singly kept missing
@@ -400,7 +400,7 @@ getting annotations for final partition
400
400
  reading output
401
401
  read 12 hmm output lines with 17 sequences in 12 events (0 failures)
402
402
  hmm step time: 0.3
403
- total time: 1.9
403
+ total time: 2.0
404
404
  partition igk:
405
405
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
406
406
  run partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/input-seqs-igk.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -552,7 +552,7 @@ hmm
552
552
  N clusters with all seqs:
553
553
  h 12 --> 1 -11
554
554
  k 2 --> 1 -1
555
- total time: 9.4
555
+ total time: 9.5
556
556
  get-selection-metrics-new-simu partis get-selection-metrics --dont-write-git-info --paired-loci --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
557
557
  get-selection-metrics igh+igk: igh
558
558
  run partis get-selection-metrics --locus igh --dont-write-git-info --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv --refuse-to-cache-parameters --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml
@@ -632,7 +632,7 @@ hmm
632
632
  starting 2 jobs
633
633
  run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/input-seqs.fa
634
634
  run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/input-seqs.fa
635
- made 2 fasttree trees (0.0s)
635
+ made 2 fasttree trees (0.1s)
636
636
  tree origins: 2 ran fasttree
637
637
  setting default tau to 1 / 334 = 0.0030
638
638
  calculating normalized lb index and lb ratio and lb fraction with tau 0.0030
@@ -673,10 +673,10 @@ hmm
673
673
  skipped 1/4 clusters that had no uids in common with tree
674
674
  writing selection metrics to test/paired/new-results/partition-new-simu/selection-metrics.yaml
675
675
  writing 10 chosen abs to test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
676
- total time: 5.7
676
+ total time: 5.8
677
677
  cache-parameters-data partis cache-parameters --dont-write-git-info --paired-loci --infname test/paired-data/all-seqs.fa --parameter-dir test/paired/new-results/test/parameters/data --n-max-queries 100 --random-seed 1 --n-procs 10
678
678
  note: --paired-outdir is not set, so there will be no persistent record of the results (except the parameter directory).
679
- run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/243911/meta.yaml --n-max-queries 100
679
+ run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/400051/meta.yaml --n-max-queries 100
680
680
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
681
681
  extract_pairing_info(): read 100 sequences with 48 droplet ids
682
682
  droplet id separators (set automatically): _ indices: [0]
@@ -687,9 +687,9 @@ hmm
687
687
  2 42 0.875
688
688
  3 2 0.042
689
689
  4 2 0.042
690
- run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/243911 --input-metafname /tmp/runner/hmms/243911/meta.yaml --n-max-queries 100
690
+ run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/400051 --input-metafname /tmp/runner/hmms/400051/meta.yaml --n-max-queries 100
691
691
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
692
- --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/243911/meta.yaml: paired-uids
692
+ --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/400051/meta.yaml: paired-uids
693
693
  read pairing info for 100 seqs from input meta file
694
694
  running vsearch on 100 sequences:
695
695
  igh: 49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
@@ -712,10 +712,10 @@ totals: igh 48 igk 37 igl 15
712
712
  2 0.13 h l
713
713
  1 0.07 h k
714
714
  1 0.07 h h k
715
- writing to /tmp/runner/hmms/243911/
716
- igh: 48 to 243911/igh.fa
717
- igk: 37 to 243911/igk.fa
718
- igl: 15 to 243911/igl.fa
715
+ writing to /tmp/runner/hmms/400051/
716
+ igh: 48 to 400051/igh.fa
717
+ igk: 37 to 400051/igk.fa
718
+ igl: 15 to 400051/igl.fa
719
719
  writing to paired subdirs
720
720
  igh+igk:
721
721
  igh: 36 / 48 to igh+igk/igh.fa
@@ -724,8 +724,8 @@ writing to paired subdirs
724
724
  igh: 15 / 48 to igh+igl/igh.fa
725
725
  igl: 15 / 15 to igh+igl/igl.fa
726
726
  cache-parameters igh:
727
- run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/243911/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/243911/meta.yaml
728
- --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/243911/meta.yaml: paired-uids
727
+ run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/400051/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/400051/meta.yaml
728
+ --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/400051/meta.yaml: paired-uids
729
729
  caching parameters
730
730
  vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.0 sec
731
731
  keeping 23 / 198 v genes
@@ -748,15 +748,15 @@ smith-waterman (writing parameters)
748
748
  hmm
749
749
  reading output
750
750
  read 48 hmm output lines with 48 sequences in 48 events (0 failures)
751
- writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (2.0 sec)
752
- infra time: 2.1
753
- hmm step time: 3.1
751
+ writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (1.9 sec)
752
+ infra time: 2.0
753
+ hmm step time: 3.0
754
754
  writing hmms removed 1 genes from glfo (leaving v 23 d 18 j 6)
755
755
  (0.9 sec)
756
756
  total time: 7.5
757
757
  cache-parameters igk:
758
- run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/243911/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/243911/meta.yaml
759
- --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/243911/meta.yaml: paired-uids
758
+ run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/400051/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/400051/meta.yaml
759
+ --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/400051/meta.yaml: paired-uids
760
760
  caching parameters
761
761
  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.0 sec
762
762
  keeping 16 / 64 v genes
@@ -772,22 +772,22 @@ smith-waterman (writing parameters)
772
772
  info for 37 / 37 = 1.000 (removed: 0 failed)
773
773
  kept 1 (0.027) unproductive
774
774
  writing sw results to test/paired/new-results/test/parameters/data/igk/sw-cache.yaml
775
- writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.4 sec)
776
- water time: 1.5 (ig-sw 1.5 processing 0.1)
775
+ writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.3 sec)
776
+ water time: 1.5 (ig-sw 1.4 processing 0.1)
777
777
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
778
- (1.0 sec)
778
+ (1.1 sec)
779
779
  hmm
780
780
  reading output
781
781
  read 37 hmm output lines with 37 sequences in 37 events (0 failures)
782
- writing parameters to test/paired/new-results/test/parameters/data/igk/hmm (1.4 sec)
783
- infra time: 1.4
784
- hmm step time: 2.0
782
+ writing parameters to test/paired/new-results/test/parameters/data/igk/hmm (1.3 sec)
783
+ infra time: 1.3
784
+ hmm step time: 1.9
785
785
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
786
- (1.0 sec)
787
- total time: 5.9
786
+ (1.1 sec)
787
+ total time: 5.8
788
788
  cache-parameters igl:
789
- run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/243911/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/243911/meta.yaml
790
- --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/243911/meta.yaml: paired-uids
789
+ run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/400051/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/400051/meta.yaml
790
+ --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/400051/meta.yaml: paired-uids
791
791
  caching parameters
792
792
  vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.0 sec
793
793
  keeping 10 / 80 v genes
@@ -802,9 +802,9 @@ smith-waterman (writing parameters)
802
802
  info for 15 / 15 = 1.000 (removed: 0 failed)
803
803
  writing sw results to test/paired/new-results/test/parameters/data/igl/sw-cache.yaml
804
804
  writing parameters to test/paired/new-results/test/parameters/data/igl/sw (0.9 sec)
805
- water time: 1.0 (ig-sw 1.0 processing 0.0)
805
+ water time: 0.9 (ig-sw 0.9 processing 0.0)
806
806
  writing hmms removed 6 genes from glfo (leaving v 10 d 1 j 3)
807
- (0.6 sec)
807
+ (0.7 sec)
808
808
  hmm
809
809
  reading output
810
810
  read 15 hmm output lines with 15 sequences in 15 events (0 failures)
@@ -812,7 +812,7 @@ hmm
812
812
  infra time: 0.8
813
813
  hmm step time: 1.1
814
814
  writing hmms removed 0 genes from glfo (leaving v 10 d 1 j 3)
815
- (0.6 sec)
816
- total time: 3.5
817
- warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/243911/: failed.fa
815
+ (0.7 sec)
816
+ total time: 3.6
817
+ warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/400051/: failed.fa
818
818
  total time: 22.1
test/phylo-naive-run.py CHANGED
@@ -32,7 +32,7 @@ parser = argparse.ArgumentParser(formatter_class=MultiplyInheritedFormatter, des
32
32
  parser.add_argument('--input-partition-dir', required=True, help='dir with partis partition output')
33
33
  parser.add_argument('--outdir', required=True, help='if set, read simulation from this file and compare to results')
34
34
  parser.add_argument('--simdir', help='if set, read simulation from this file and compare to results')
35
- parser.add_argument('--phylo-naive-inference-fuzz')
35
+ parser.add_argument('--phylo-naive-inference-fuzz', type=int, default=1)
36
36
  parser.add_argument('--tree-inference-method', required=True)
37
37
  parser.add_argument('--n-procs') # not used atm
38
38
  parser.add_argument('--debug', action='store_true')