Phase 1: Disjoint grouping core implementation

bin/partis

@@ -37,6 +37,7 @@ import partis.seqfileopener as seqfileopener
 from partis.partitiondriver import PartitionDriver
 from partis.clusterpath import ClusterPath
 import partis.paircluster as paircluster
+import partis.disjointgrouper as disjointgrouper
 from partis.parametercounter import ParameterCounter
 from partis.corrcounter import CorrCounter
 from partis.waterer import Waterer
@@ -1660,6 +1661,8 @@ subconfig = collections.OrderedDict((
     ('get-linearham-info', {'func' : run_partitiondriver, 'help' : 'Write input file for linearham (to --linearham-info-fname), using a previous partis output (--outfname) file as input.'}),
     ('update-meta-info',   {'func' : run_partitiondriver, 'help' : 'Read existing output files and update their info from --input-metafnames, i.e. if your input meta info changed but you don\'t want to rerun everything. Also updates --queries-to-include info.'}),
     ('write-fake-paired-annotations',   {'func' : run_partitiondriver, 'help' : 'Read paired output from --paired-outdir, and write \'fake\' annotations by concatenating h and l seqs to file in the same dir (useful e.g. for phylo method input).'}),
+    ('disjoint-group',    {'func' : disjointgrouper.run_disjoint_group, 'help' : 'Split sequences into disjoint groups by cdr3 length, writing per-group fastas and a manifest yaml to --outdir. Auto-runs sw annotation if --parameter-dir is not set.'}),
+    ('assemble-groups',   {'func' : disjointgrouper.run_assemble_groups, 'help' : 'Validate and merge per-group partition outputs from disjoint grouping. Reads manifest from --disjoint-dir, reconciles germline info, checks sequence count invariants and uid uniqueness, and writes a single merged partition yaml per locus. Use --no-merge-output to keep per-group files separate for large datasets.'}),
     # deprecated actions:
     ('view-annotations' , {'func' : run_partitiondriver, 'help' : 'Mostly deprecated: Print annotations from an existing old-style annotation output csv (for current yaml output files, use \'view-output\').'}),
     ('view-partitions'  , {'func' : run_partitiondriver, 'help' : 'Mostly deprecated: Print partitions from an existing old-style partition output csv (for current yaml output files, use \'view-output\').'}),
@@ -1800,6 +1803,10 @@ subargs['plot-partitions'].append({'name' : '--seed-loci', 'kwargs' : {'help' :
 
 subargs['get-linearham-info'].append({'name' : '--linearham-info-fname', 'kwargs' : {'help' : 'yaml file to which to write linearhmam input information'}})
 
+subargs['disjoint-group'].append({'name' : '--disjoint-dir', 'kwargs' : {'help' : 'Working directory for disjoint grouping. Step 1 writes manifest + per-group fastas here, step 2 writes per-group partition yamls here, step 3 reads from here.'}})
+subargs['assemble-groups'].append({'name' : '--disjoint-dir', 'kwargs' : {'help' : 'Working directory for disjoint grouping (same directory used for disjoint-group step 1 and partition step 2).'}})
+subargs['assemble-groups'].append({'name' : '--no-merge-output', 'kwargs' : {'action' : 'store_true', 'help' : 'Skip writing merged single-yaml output; keep per-group partition files separate (for large datasets where a single multi-GB yaml is impractical).'}})
+
 sub_arg_groups = {'subset-partition' : ['partition'], 'subset-annotate' : ['annotate']}  # actions that use the args of other actions (i.e. their <subargs> need to be merged, e.g. 'subset-partition' needs access to all the args of 'partition')
 
 def get_arg_names(actions):  # return set of all arg names (in the form they appear in args.__dict__) for the specified actions

partis/processargs.py

@@ -12,7 +12,7 @@
 def get_dummy_outfname(workdir, locus=None):
     return '%s/XXX-dummy-simu%s.yaml' % (workdir, '-'+locus if locus is not None else '')
 
-actions_not_requiring_input = ['simulate', 'view-output', 'merge-paired-partitions', 'view-annotations', 'view-partitions', 'view-cluster-annotations', 'plot-partitions', 'view-alternative-annotations', 'get-selection-metrics', 'get-linearham-info', 'write-fake-paired-annotations']
+actions_not_requiring_input = ['simulate', 'view-output', 'merge-paired-partitions', 'view-annotations', 'view-partitions', 'view-cluster-annotations', 'plot-partitions', 'view-alternative-annotations', 'get-selection-metrics', 'get-linearham-info', 'write-fake-paired-annotations', 'disjoint-group', 'assemble-groups']
 
 # ----------------------------------------------------------------------------------------
 # split this out so we can call it from both bin/partis and bin/test-germline-inference.py

test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/igh.fa

@@ -0,0 +1,2 @@
+>AAACGGGAGAAACGCC-1_contig_1
+GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGTAACCTCCGGATTCACCTTCAGTAGCTACTGGATGAACTGGGTCCGCCAAGTTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATCCTAATGGAGATTACAAAAACTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTATATCTGCAAATGAACAGTCTGGGAGTCGAGGACACAGCTATATATTACTGTGCAAGGGAGGGGTGGGGTGACTTCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCGG

test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/igk.fa

@@ -0,0 +1,12 @@
+>AAACCTGGTAACGCGA-1_contig_2
+GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC
+>AAACCTGGTCAACATC-1_contig_2
+GAAATTGTGTTGACACAATCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTTCTTAGCCTGGTATCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTCTGATACATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCATCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTCGCAACTGGCCCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC
+>AAACGGGAGATAGCAT-1_contig_2
+GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATCATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC
+>AAACGGGAGGCCCTTG-1_contig_2
+GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC
+>AAAGATGCAATGTAAG-1_contig_2
+GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC
+>AAAGATGCATCGTCGG-1_contig_2
+GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAACTTTTTACATTGGTATCAGCAAAAACCAGGGAAAGCCCCTAACCTCCTGATCTATGCTGCATCCAGCTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTATGCAACTTACTACTGTCAACAGACTTACAGTACCCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC

test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/partition-igh.yaml

@@ -0,0 +1 @@
+{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -177.6178579483573, "n_clusters": 1, "n_procs": 1, "partition": [["AAACGGGAGAAACGCC-1_contig_1"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGAAACGCC-1_contig_1"], "invalid": false, "v_gene": "IGHV3-74*01", "d_gene": "IGHD1-26*01", "j_gene": "IGHJ4*02", "cdr3_length": 30, "mature_cdr3_lengths": [30], "mut_freqs": [0.06936416184971098], "n_mutations": [24], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGTAACCTCCGGATTCACCTTCAGTAGCTACTGGATGAACTGGGTCCGCCAAGTTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATCCTAATGGAGATTACAAAAACTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTATATCTGCAAATGAACAGTCTGGGAGTCGAGGACACAGCTATATATTACTGTGCAAGGGAGGGGTGGGGTGACTTCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCGG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGAGGGGTGGGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-74*01": 1.0}, "d_per_gene_support": {"IGHD1-26*01": 0.3474119780591844, "IGHD2-21*01": 0.239648755444251, "IGHD2-15*01": 0.20105154789523053, "IGHD3-3*01": 0.19788980440739046, "IGHD3-16*03": 0.013997914193956247}, "j_per_gene_support": {"IGHJ4*02": 0.999999515548499, "IGHJ5*02": 4.844515142301888e-07}, "v_3p_del": 0, "d_5p_del": 6, "d_3p_del": 9, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGG", "dj_insertion": "G", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 312}}]}