partis-bcr 1.0.10__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 (44) hide show
  1. bin/parse-output.py +2 -2
  2. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/parse-output.py +2 -2
  3. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/RECORD +44 -44
  5. test/new-results/test.log +2 -2
  6. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +3 -3
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  8. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +2 -2
  9. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  10. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  11. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  24. test/paired/new-results/run-times.csv +6 -6
  25. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +6 -10
  26. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +7 -11
  27. test/paired/new-results/subset-partition-new-simu/merged-partition.log +4 -8
  28. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  29. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  30. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  31. test/paired/new-results/test.log +35 -44
  32. test/phylo-naive-run.py +1 -1
  33. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  34. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  35. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  36. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  37. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/gctree-run.py +0 -0
  38. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  39. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/partis-test.py +0 -0
  40. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/split-loci.py +0 -0
  41. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/WHEEL +0 -0
  42. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/entry_points.txt +0 -0
  43. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/licenses/COPYING +0 -0
  44. {partis_bcr-1.0.10.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": "v1.0.10"}}, "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
@@ -21,7 +21,7 @@ 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
26
  (0.6 sec)
27
27
  hmm
@@ -32,8 +32,8 @@ hmm
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)
36
- total time: 4.1
35
+ (0.3 sec)
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)
39
39
  run partis cache-parameters --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/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
@@ -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: 12.7
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:
@@ -131,14 +131,14 @@ hmm
131
131
  29 clusters with 2 procs (0.5s)
132
132
  23 clusters with 1 proc (0.6s)
133
133
  note not merging entire cpath history
134
- partition loop time: 2.9
134
+ partition loop time: 2.8
135
135
  getting annotations for final partition
136
136
  subcluster annotating 20 clusters with steps: (0.7s) (0.2s) plotting performance
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
140
  subcluster annotation time 1.0
141
- total time: 5.1
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
@@ -165,7 +165,7 @@ 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
167
  subcluster annotation time 0.5
168
- total time: 1.6
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)
171
171
  run partis partition --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igl --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/ref-results/test/simu/igl.yaml --outfname test/paired/new-results/partition-new-simu/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -228,7 +228,6 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
228
228
  joint 0.963 0.594
229
229
  merge time 0.0
230
230
  need to get annotations for 7/15 joint igh clusters
231
- tag: v1.0.10
232
231
  annotate igh+igk: igh
233
232
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
234
233
  run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igh-only-partition.yaml
@@ -246,7 +245,6 @@ hmm
246
245
  subcluster annotation time 0.6
247
246
  total time: 0.6
248
247
  need to get annotations for 13/15 joint igk clusters
249
- tag: v1.0.10
250
248
  annotate igh+igk: igk
251
249
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
252
250
  run partis annotate --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igk.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igk-only-partition.yaml
@@ -288,7 +286,6 @@ hmm
288
286
  joint 1.000 0.611
289
287
  merge time 0.0
290
288
  need to get annotations for 5/8 joint igh clusters
291
- tag: v1.0.10
292
289
  annotate igh+igl: igh
293
290
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
294
291
  run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igh-only-partition.yaml
@@ -306,7 +303,6 @@ hmm
306
303
  subcluster annotation time 0.4
307
304
  total time: 0.5
308
305
  need to get annotations for 8/8 joint igl clusters
309
- tag: v1.0.10
310
306
  annotate igh+igl: igl
311
307
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
312
308
  run partis annotate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igl.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igl-only-partition.yaml
@@ -335,7 +331,7 @@ hmm
335
331
  h 20 --> 23 +3
336
332
  k 6 --> 15 +9
337
333
  l 3 --> 8 +5
338
- total time: 21.1
334
+ total time: 20.9
339
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
340
336
  note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
341
337
  --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -364,12 +360,9 @@ hmm
364
360
  writing merged outputs from 2 subsets to test/paired/new-results/subset-partition-new-simu/merged-subsets
365
361
  writing combined h/l info to fasta and meta files in test/paired/new-results/subset-partition-new-simu/merged-subsets
366
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
367
- tag: v1.0.10
368
- tag: v1.0.10
369
- tag: v1.0.10
370
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
371
364
  log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
372
- total time: 73.2
365
+ total time: 71.1
373
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
374
367
  removing seqs very different from seed seq
375
368
  wrong/no removed singly kept missing
@@ -430,7 +423,7 @@ hmm
430
423
  getting annotations for final partition
431
424
  subcluster annotating 2 clusters with steps: (0.1s) (0.1s) (0.1s)
432
425
  subcluster annotation time 0.2
433
- total time: 0.7
426
+ total time: 0.6
434
427
  partition igl:
435
428
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
436
429
  run partis partition --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --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-igl.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -492,7 +485,6 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
492
485
  merge time 0.0
493
486
  removed 7 unseeded clusters (of 8 total, leaving 1) from igh joint partition
494
487
  seed cluster size in best joint partition: 1, excluding seed seq: 0
495
- tag: v1.0.10
496
488
  annotate igh+igk: igh
497
489
  removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
498
490
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -514,7 +506,6 @@ hmm
514
506
  removed 7 unseeded clusters (of 8 total, leaving 1) from igk joint partition
515
507
  need to get annotations for 1/1 joint igk clusters
516
508
  seed cluster size in best joint partition: 1, excluding seed seq: 0
517
- tag: v1.0.10
518
509
  annotate igh+igk: igk
519
510
  removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
520
511
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -561,7 +552,7 @@ hmm
561
552
  N clusters with all seqs:
562
553
  h 12 --> 1 -11
563
554
  k 2 --> 1 -1
564
- total time: 9.9
555
+ total time: 9.5
565
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
566
557
  get-selection-metrics igh+igk: igh
567
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
@@ -641,7 +632,7 @@ hmm
641
632
  starting 2 jobs
642
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
643
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
644
- made 2 fasttree trees (0.0s)
635
+ made 2 fasttree trees (0.1s)
645
636
  tree origins: 2 ran fasttree
646
637
  setting default tau to 1 / 334 = 0.0030
647
638
  calculating normalized lb index and lb ratio and lb fraction with tau 0.0030
@@ -682,10 +673,10 @@ hmm
682
673
  skipped 1/4 clusters that had no uids in common with tree
683
674
  writing selection metrics to test/paired/new-results/partition-new-simu/selection-metrics.yaml
684
675
  writing 10 chosen abs to test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
685
- total time: 6.0
676
+ total time: 5.8
686
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
687
678
  note: --paired-outdir is not set, so there will be no persistent record of the results (except the parameter directory).
688
- run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/720767/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
689
680
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
690
681
  extract_pairing_info(): read 100 sequences with 48 droplet ids
691
682
  droplet id separators (set automatically): _ indices: [0]
@@ -696,9 +687,9 @@ hmm
696
687
  2 42 0.875
697
688
  3 2 0.042
698
689
  4 2 0.042
699
- run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/720767 --input-metafname /tmp/runner/hmms/720767/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
700
691
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
701
- --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/720767/meta.yaml: paired-uids
692
+ --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/400051/meta.yaml: paired-uids
702
693
  read pairing info for 100 seqs from input meta file
703
694
  running vsearch on 100 sequences:
704
695
  igh: 49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
@@ -721,10 +712,10 @@ totals: igh 48 igk 37 igl 15
721
712
  2 0.13 h l
722
713
  1 0.07 h k
723
714
  1 0.07 h h k
724
- writing to /tmp/runner/hmms/720767/
725
- igh: 48 to 720767/igh.fa
726
- igk: 37 to 720767/igk.fa
727
- igl: 15 to 720767/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
728
719
  writing to paired subdirs
729
720
  igh+igk:
730
721
  igh: 36 / 48 to igh+igk/igh.fa
@@ -733,8 +724,8 @@ writing to paired subdirs
733
724
  igh: 15 / 48 to igh+igl/igh.fa
734
725
  igl: 15 / 15 to igh+igl/igl.fa
735
726
  cache-parameters igh:
736
- run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/720767/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/720767/meta.yaml
737
- --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/720767/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
738
729
  caching parameters
739
730
  vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.0 sec
740
731
  keeping 23 / 198 v genes
@@ -757,15 +748,15 @@ smith-waterman (writing parameters)
757
748
  hmm
758
749
  reading output
759
750
  read 48 hmm output lines with 48 sequences in 48 events (0 failures)
760
- writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (2.0 sec)
751
+ writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (1.9 sec)
761
752
  infra time: 2.0
762
- hmm step time: 3.1
753
+ hmm step time: 3.0
763
754
  writing hmms removed 1 genes from glfo (leaving v 23 d 18 j 6)
764
- (1.0 sec)
765
- total time: 7.7
755
+ (0.9 sec)
756
+ total time: 7.5
766
757
  cache-parameters igk:
767
- run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/720767/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/720767/meta.yaml
768
- --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/720767/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
769
760
  caching parameters
770
761
  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.0 sec
771
762
  keeping 16 / 64 v genes
@@ -781,7 +772,7 @@ smith-waterman (writing parameters)
781
772
  info for 37 / 37 = 1.000 (removed: 0 failed)
782
773
  kept 1 (0.027) unproductive
783
774
  writing sw results to test/paired/new-results/test/parameters/data/igk/sw-cache.yaml
784
- writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.4 sec)
775
+ writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.3 sec)
785
776
  water time: 1.5 (ig-sw 1.4 processing 0.1)
786
777
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
787
778
  (1.1 sec)
@@ -793,10 +784,10 @@ hmm
793
784
  hmm step time: 1.9
794
785
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
795
786
  (1.1 sec)
796
- total time: 5.9
787
+ total time: 5.8
797
788
  cache-parameters igl:
798
- run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/720767/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/720767/meta.yaml
799
- --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/720767/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
800
791
  caching parameters
801
792
  vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.0 sec
802
793
  keeping 10 / 80 v genes
@@ -823,5 +814,5 @@ hmm
823
814
  writing hmms removed 0 genes from glfo (leaving v 10 d 1 j 3)
824
815
  (0.7 sec)
825
816
  total time: 3.6
826
- warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/720767/: failed.fa
827
- total time: 22.9
817
+ warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/400051/: failed.fa
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')