Pygor Tutorial

Welcome to the pygor3 Tutorial.

Pygor3 is an open source project and Python package that allows to analyze infer, evaluate and generate V(D)J sequences, by using IGoR’s.

Pygor3 could help you to get simple calculations and visualizations of the statistics in VDJ recombination

Introduction

An IGoR model’s encapsulates the Bayesian network probabilistic parameters of a V(D)J recombination process. IGoR is shipped with a set of default models.

As an example lets load the recombination model for a human \(\beta\) T-cell receptor

Loading default IgorModel

import pygor3 as p3
mdl_hb = p3.get_default_IgorModel("human", "tcr_beta")

Reading Parms filename from:  /home/olivares/.local/share/igor/models/human/tcr_beta/models/model_parms.txt
Reading Marginals filename from:  /home/olivares/.local/share/igor/models/human/tcr_beta/models/model_marginals.txt

mdl_hb

<pygor3.IgorIO.IgorModel at 0x7f8568eeacd0>

Conditional probabilites

mdl_hb.export_plot_Pconditionals('hb_CP')

P_J_g_V = mdl_hb['j_choice']
P_J_g_V

<xarray.DataArray (v_choice: 89, j_choice: 15)>
array([[1.28586e-01, 1.04003e-01, 4.10916e-02, ..., 0.00000e+00,
        5.36364e-02, 3.73186e-02],
       [1.66126e-01, 7.89615e-02, 1.13701e-02, ..., 2.46074e-02,
        6.49049e-02, 7.46140e-02],
       [1.66156e-01, 7.90103e-02, 1.13744e-02, ..., 2.45354e-02,
        6.49334e-02, 7.46554e-02],
       ...,
       [1.24050e-01, 4.76394e-02, 0.00000e+00, ..., 3.52196e-02,
        5.51254e-02, 6.01472e-02],
       [3.64941e-06, 2.04721e-09, 0.00000e+00, ..., 3.41728e-01,
        6.84855e-02, 8.22442e-02],
       [1.06077e-01, 1.13773e-01, 4.03129e-02, ..., 2.20679e-02,
        7.16947e-02, 5.81105e-02]])
Coordinates:
  * v_choice       (v_choice) int64 0 1 2 3 4 5 6 7 ... 81 82 83 84 85 86 87 88
    lbl__v_choice  (v_choice) <U11 'TRBV1*01' 'TRBV10-1*01' ... 'TRBV9*01'
    seq__v_choice  (v_choice) object 'GATACTGGAATTACCCAGACACCAAAATACCTGGTCACA...
  * j_choice       (j_choice) int64 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
    lbl__j_choice  (j_choice) <U10 'TRBJ1-1*01' 'TRBJ1-2*01' ... 'TRBJ2-7*02'
    seq__j_choice  (j_choice) object 'TGAACACTGAAGCTTTCTTTGGACAAGGCACCAGACTCA...
Attributes:
    nickname:    j_choice
    event_type:  GeneChoice
    seq_type:    J_gene
    seq_side:    Undefined_side
    priority:    7
    parents:     ['v_choice']
    childs:      ['j_5_del', 'd_gene']

xarray.DataArray

• v_choice: 89
• j_choice: 15

• 0.1286 0.104 0.04109 0.01281 ... 0.08853 0.02207 0.07169 0.05811

  array([[1.28586e-01, 1.04003e-01, 4.10916e-02, ..., 0.00000e+00,
          5.36364e-02, 3.73186e-02],
         [1.66126e-01, 7.89615e-02, 1.13701e-02, ..., 2.46074e-02,
          6.49049e-02, 7.46140e-02],
         [1.66156e-01, 7.90103e-02, 1.13744e-02, ..., 2.45354e-02,
          6.49334e-02, 7.46554e-02],
         ...,
         [1.24050e-01, 4.76394e-02, 0.00000e+00, ..., 3.52196e-02,
          5.51254e-02, 6.01472e-02],
         [3.64941e-06, 2.04721e-09, 0.00000e+00, ..., 3.41728e-01,
          6.84855e-02, 8.22442e-02],
         [1.06077e-01, 1.13773e-01, 4.03129e-02, ..., 2.20679e-02,
          7.16947e-02, 5.81105e-02]])

• Coordinates: (6)
  • v_choice
    (v_choice)
    int64
    0 1 2 3 4 5 6 ... 83 84 85 86 87 88

    array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16, 17,
           18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
           36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
           54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
           72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88])

  • lbl__v_choice
    (v_choice)
    <U11
    'TRBV1*01' ... 'TRBV9*01'

    array(['TRBV1*01', 'TRBV10-1*01', 'TRBV10-1*02', 'TRBV10-1*04',
           'TRBV10-2*01', 'TRBV10-3*01', 'TRBV10-3*02', 'TRBV11-1*01',
           'TRBV11-2*01', 'TRBV11-2*02', 'TRBV11-2*03', 'TRBV11-3*01',
           'TRBV12-1*01', 'TRBV12-2*01', 'TRBV12-3*01', 'TRBV12-4*01',
           'TRBV12-4*02', 'TRBV12-5*01', 'TRBV13*01', 'TRBV14*01',
           'TRBV15*01', 'TRBV15*02', 'TRBV15*03', 'TRBV16*01', 'TRBV17*01',
           'TRBV18*01', 'TRBV19*01', 'TRBV2*01', 'TRBV2*03', 'TRBV20-1*01',
           'TRBV23-1*01', 'TRBV24-1*01', 'TRBV25-1*01', 'TRBV26*01',
           'TRBV27*01', 'TRBV28*01', 'TRBV29-1*01', 'TRBV29-1*02',
           'TRBV3-1*01', 'TRBV3-1*02', 'TRBV3-2*01', 'TRBV3-2*02',
           'TRBV30*01', 'TRBV30*02', 'TRBV30*04', 'TRBV4-1*01', 'TRBV4-2*01',
           'TRBV4-3*01', 'TRBV4-3*02', 'TRBV5-1*01', 'TRBV5-3*01',
           'TRBV5-3*02', 'TRBV5-4*01', 'TRBV5-4*02', 'TRBV5-5*01',
           'TRBV5-6*01', 'TRBV5-7*01', 'TRBV5-8*01', 'TRBV6-1*01',
           'TRBV6-2*01', 'TRBV6-3*01', 'TRBV6-4*01', 'TRBV6-5*01',
           'TRBV6-6*01', 'TRBV6-6*02', 'TRBV6-7*01', 'TRBV6-8*01',
           'TRBV6-9*01', 'TRBV7-1*01', 'TRBV7-2*01', 'TRBV7-2*02',
           'TRBV7-2*03', 'TRBV7-2*05', 'TRBV7-3*01', 'TRBV7-3*02',
           'TRBV7-3*03', 'TRBV7-3*04', 'TRBV7-4*01', 'TRBV7-6*01',
           'TRBV7-7*01', 'TRBV7-7*03', 'TRBV7-8*01', 'TRBV7-8*02',
           'TRBV7-9*01', 'TRBV7-9*04', 'TRBV7-9*05', 'TRBV7-9*06',
           'TRBV7-9*07', 'TRBV9*01'], dtype='<U11')

  • seq__v_choice
    (v_choice)
    object
    'GATACTGGAATTACCCAGACACCAAAATACC...

    array(['GATACTGGAATTACCCAGACACCAAAATACCTGGTCACAGCAATGGGGAGTAAAAGGACAATGAAACGTGAGCATCTGGGACATGATTCTATGTATTGGTACAGACAGAAAGCTAAGAAATCCCTGGAGTTCATGTTTTACTACAACTGTAAGGAATTCATTGAAAACAAGACTGTGCCAAATCACTTCACACCTGAATGCCCTGACAGCTCTCGCTTATACCTTCATGTGGTCGCACTGCAGCAAGAAGACTCAGCTGCGTATCTCTGCACCAGCAGCCAAGA',
           'GATGCTGAAATCACCCAGAGCCCAAGACACAAGATCACAGAGACAGGAAGGCAGGTGACCTTGGCGTGTCACCAGACTTGGAACCACAACAATATGTTCTGGTATCGACAAGACCTGGGACATGGGCTGAGGCTGATCCATTACTCATATGGTGTTCAAGACACTAACAAAGGAGAAGTCTCAGATGGCTACAGTGTCTCTAGATCAAACACAGAGGACCTCCCCCTCACTCTGGAGTCTGCTGCCTCCTCCCAGACATCTGTATATTTCTGCGCCAGCAGTGAGTC',
           'GATGCTGAAATCACCCAGAGCCCAAGACACAAGATCACAGAGACAGGAAGGCAGGTGACCTTGGCGTGTCACCAGACTTGGAACCACAACAATATGTTCTGGTATCGACAAGACCTGGGACATGGGCTGAGGCTGATCCATTACTCATATGGTGTTCACGACACTAACAAAGGAGAAGTCTCAGATGGCTACAGTGTCTCTAGATCAAACACAGAGGACCTCCCCCTCACTCTGGAGTCTGCTGCCTCCTCCCAGACATCTGTATATTTCTGCGCCAGCAGTGAGTC',
           'GATGCTGAAATCACCCAGAGCCCAAGACACAAGATCACAGAGACAGGAAGGCAGGTGACCTTGGCGTGTCACCAGACTTGGAACCACAACAATATGTTCTGGTATCGACAAGACCTGGGACATGGGCTGAGGCTGATCCATTACTCATATGGTGTTCACGACACTAACAAAGGAGAAGTCTCAGATGGCTACAGTGTCTCTAGATCAAACACAGAGGACCTCCCCCTCACTCTGTAGTCTGCTGCCTCCTCCCAGACATCTGTATATTTCTGCGCCAGCAGTGAGTC',
           'GATGCTGGAATCACCCAGAGCCCAAGATACAAGATCACAGAGACAGGAAGGCAGGTGACCTTGATGTGTCACCAGACTTGGAGCCACAGCTATATGTTCTGGTATCGACAAGACCTGGGACATGGGCTGAGGCTGATCTATTACTCAGCAGCTGCTGATATTACAGATAAAGGAGAAGTCCCCGATGGCTATGTTGTCTCCAGATCCAAGACAGAGAATTTCCCCCTCACTCTGGAGTCAGCTACCCGCTCCCAGACATCTGTGTATTTCTGCGCCAGCAGTGAGTC',
           'GATGCTGGAATCACCCAGAGCCCAAGACACAAGGTCACAGAGACAGGAACACCAGTGACTCTGAGATGTCACCAGACTGAGAACCACCGCTATATGTACTGGTATCGACAAGACCCGGGGCATGGGCTGAGGCTGATCCATTACTCATATGGTGTTAAAGATACTGACAAAGGAGAAGTCTCAGATGGCTATAGTGTCTCTAGATCAAAGACAGAGGATTTCCTCCTCACTCTGGAGTCCGCTACCAGCTCCCAGACATCTGTGTACTTCTGTGCCATCAGTGAGTC',
           'GCTGGAATCACCCAGAGCCCAAGACACAAGGTCACAGAGACAGGAACACCAGTGACTCTGAGATGTCATCAGACTGAGAACCACCGCTATATGTACTGGTATCGACAAGACCCGGGGCATGGGCTGAGGCTGATCCATTACTCATATGGTGTTAAAGATACTGACAAAGGAGAAGTCTCAGATGGCTATAGTGTCTCTAGATCAAAGACAGAGGATTTCCTCCTCACTCTGGAGTCCGCTACCAGCTCCCAGACATCTGTGTACTTCTGTGCCATCAGTGAGTC',
           'GAAGCTGAAGTTGCCCAGTCCCCCAGATATAAGATTACAGAGAAAAGCCAGGCTGTGGCTTTTTGGTGTGATCCTATTTCTGGCCATGCTACCCTTTACTGGTACCGGCAGATCCTGGGACAGGGCCCGGAGCTTCTGGTTCAATTTCAGGATGAGAGTGTAGTAGATGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAGCCTGCAGAGCTTGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'GAAGCTGGAGTTGCCCAGTCTCCCAGATATAAGATTATAGAGAAAAGGCAGAGTGTGGCTTTTTGGTGCAATCCTATATCTGGCCATGCTACCCTTTACTGGTACCAGCAGATCCTGGGACAGGGCCCAAAGCTTCTGATTCAGTTTCAGAATAACGGTGTAGTGGATGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAGCCTGCAAAGCTTGAGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGA',
           'GAAGCTGGAGTTGCCCAGTCTCCCAGATATAAGATTATAGAGAAAAGGCAGAGTGTGGCTTTTTGGTGCAATCCTATATCTGGCCATGCTACCCTTTACTGGTACCAGCAGATCCTGGGACAGGGCCCAAAGCTTCTGATTCAGTTTCAGAATAACGGTGTAGTGGATGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAGCCTGCAAAGCTTGAGAACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGA',
           'GAAGCTGGAGTTGCCCAGTCTCCCAGATATAAGATTATAGAGAAAAGGCAGAGTGTGGCTTTTTGGTGCAATCCTATATCTGGCCATGCTACCCTTTACTGGTACCAGCAGATCCTGGGACAGGGCCCAAAGCTTCTGATTCAGTTTCAGAATAACGGTGTAGTGGATGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAACCTGCAAAGCTTGAGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGA',
           'GAAGCTGGAGTGGTTCAGTCTCCCAGATATAAGATTATAGAGAAAAAACAGCCTGTGGCTTTTTGGTGCAATCCTATTTCTGGCCACAATACCCTTTACTGGTACCTGCAGAACTTGGGACAGGGCCCGGAGCTTCTGATTCGATATGAGAATGAGGAAGCAGTAGACGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAGCCTGCAGAGCTTGGGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGA',
           'GCTGGTGTTATCCAGTCACCCAGGCACAAAGTGACAGAGATGGGACAATCAGTAACTCTGAGATGCGAACCAATTTCAGGCCACAATGATCTTCTCTGGTACAGACAGACCTTTGTGCAGGGACTGGAATTGCTGAATTACTTCTGCAGCTGGACCCTCGTAGATGACTCAGGAGTGTCCAAGGATTGATTCTCAGCACAGATGCCTGATGTATCATTCTCCACTCTGAGGATCCAGCCCATGGAACCCAGGGACTTGGGCCTATATTTCTGTGCCAGCAGCTTTGC',
           'GCTGGCATTATCCAGTCACCCAAGCATGAGGTGACAGAAATGGGACAAACAGTGACTCTGAGATGTGAGCCAATTTTTGGCCACAATTTCCTTTTCTGGTACAGAGATACCTTCGTGCAGGGACTGGAATTGCTGAGTTACTTCCGGAGCTGATCTATTATAGATAATGCAGGTATGCCCACAGAGCGATTCTCAGCTGAGAGGCCTGATGGATCATTCTCTACTCTGAAGATCCAGCCTGCAGAGCAGGGGGACTCGGCCGTGTATGTCTGTGCAAGTCGCTTAGC',
           'GATGCTGGAGTTATCCAGTCACCCCGCCATGAGGTGACAGAGATGGGACAAGAAGTGACTCTGAGATGTAAACCAATTTCAGGCCACAACTCCCTTTTCTGGTACAGACAGACCATGATGCGGGGACTGGAGTTGCTCATTTACTTTAACAACAACGTTCCGATAGATGATTCAGGGATGCCCGAGGATCGATTCTCAGCTAAGATGCCTAATGCATCATTCTCCACTCTGAAGATCCAGCCCTCAGAACCCAGGGACTCAGCTGTGTACTTCTGTGCCAGCAGTTTAGC',
           'GATGCTGGAGTTATCCAGTCACCCCGGCACGAGGTGACAGAGATGGGACAAGAAGTGACTCTGAGATGTAAACCAATTTCAGGACACGACTACCTTTTCTGGTACAGACAGACCATGATGCGGGGACTGGAGTTGCTCATTTACTTTAACAACAACGTTCCGATAGATGATTCAGGGATGCCCGAGGATCGATTCTCAGCTAAGATGCCTAATGCATCATTCTCCACTCTGAAGATCCAGCCCTCAGAACCCAGGGACTCAGCTGTGTACTTCTGTGCCAGCAGTTTAGC',
           'GATGCTGGAGTTATCCAGTCACCCCGGCACGAGGTGACAGAGATGGGACAAGAAGTGACTCTGAGATGTAAACCAATTTCAGGACATGACTACCTTTTCTGGTACAGACAGACCATGATGCGGGGACTGGAGTTGCTCATTTACTTTAACAACAACGTTCCGATAGATGATTCAGGGATGCCCGAGGATCGATTCTCAGCTAAGATGCCTAATGCATCATTCTCCACTCTGAGGATCCAGCCCTCAGAACCCAGGGACTCAGCTGTGTACTTCTGTGCCAGCAGTTTAGC',
           'GATGCTAGAGTCACCCAGACACCAAGGCACAAGGTGACAGAGATGGGACAAGAAGTAACAATGAGATGTCAGCCAATTTTAGGCCACAATACTGTTTTCTGGTACAGACAGACCATGATGCAAGGACTGGAGTTGCTGGCTTACTTCCGCAACCGGGCTCCTCTAGATGATTCGGGGATGCCGAAGGATCGATTCTCAGCAGAGATGCCTGATGCAACTTTAGCCACTCTGAAGATCCAGCCCTCAGAACCCAGGGACTCAGCTGTGTATTTTTGTGCTAGTGGTTTGGT',
           'GCTGCTGGAGTCATCCAGTCCCCAAGACATCTGATCAAAGAAAAGAGGGAAACAGCCACTCTGAAATGCTATCCTATCCCTAGACACGACACTGTCTACTGGTACCAGCAGGGTCCAGGTCAGGACCCCCAGTTCCTCATTTCGTTTTATGAAAAGATGCAGAGCGATAAAGGAAGCATCCCTGATCGATTCTCAGCTCAACAGTTCAGTGACTATCATTCTGAACTGAACATGAGCTCCTTGGAGCTGGGGGACTCAGCCCTGTACTTCTGTGCCAGCAGCTTAGG',
           'GAAGCTGGAGTTACTCAGTTCCCCAGCCACAGCGTAATAGAGAAGGGCCAGACTGTGACTCTGAGATGTGACCCAATTTCTGGACATGATAATCTTTATTGGTATCGACGTGTTATGGGAAAAGAAATAAAATTTCTGTTACATTTTGTGAAAGAGTCTAAACAGGATGAGTCCGGTATGCCCAACAATCGATTCTTAGCTGAAAGGACTGGAGGGACGTATTCTACTCTGAAGGTGCAGCCTGCAGAACTGGAGGATTCTGGAGTTTATTTCTGTGCCAGCAGCCAAGA',
    ...
           'GGAGCTGGAGTCTCCCAGTCCCCCAGTAACAAGGTCACAGAGAAGGGAAAGGATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAGAGGCTGGGGCAGGGCCTGGAGTTTTTAATTTACTTCCAAGGCAACAGTGCACCAGACAAATCAGGGCTGCCCAGTGATCGCTTCTCTGCAGAGAGGACTGGGGAATCCGTCTCCACTCTGACGATCCAGCGCACACAGCAGGAGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGC',
           'GCTGGAGTCTCCCAGTCCCCCAGTAACAAGGTCACAGAGAAGGGAAAGGATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAGAGGCTGGGGCAGGGCCTGGAGTTTTTAATTTACTTCCAAGGCAACAGTGCACCAGACAAATCAGGGCTGCCCAGTGATCGCTTCTCTGCAGAGAGGACTGGGGAATCCGTCTCCACTCTGACGATCCAGCGCACACAGCAGGAGGACTCGGCCGTGTATCTCTGTACCAGCAGCTTAGC',
           'GGAGCTGGAGTCTCCCAGTCCCCCAGTAACAAGGTCACAGAGAAGGGAAAGGATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAGAGGCTGGGGCAGGGCCTGGAGTTTTTAATTTACTTCCAAGGCAACAGTGCACCAGACAAATCAGGGCTGCCCAGTGATCGCTTCTCTGCAGAGAGGACTGGGGAATCCGTCTCCACTCTGACGATCCAGCGCACATAGCAGGAGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGACCCCCAGTAACAAGGTCACAGAGAAGGGAAAATATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAAAGCCTGGGGCAGGGCCCAGAGTTTCTAATTTACTTCCAAGGCACGGGTGCGGCAGATGACTCAGGGCTGCCCAACGATCGGTTCTTTGCAGTCAGGCCTGAGGGATCCGTCTCTACTCTGAAGATCCAGCGCACAGAGCGGGGGGACTCAGCCGTGTATCTCTGTGCCAGCAGCTTAAC',
           'GGTGCTGGAGTCTCCCAGACCCCCAGTAACAAGGTCACAGAGAAGGGAAAAGATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAAAGCCTGGGGCAGGGCCCAGAGTTTCTAATTTACTTCCAAGGCACGGGTGCGGCAGATGACTCAGGGCTGCCCAAAGATCGGTTCTTTGCAGTCAGGCCTGAGGGATCCGTCTCTACTCTGAAGATCCAGCGCACAGAGCAGGGGGACTCAGCCGTGTATCTCCGTGCCAGCAGCTTAAC',
           'GGTGCTGGAGTCTCCCAGACCCCCAGTAACAAGGTCACAGAGAAGGGAAAAGATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAAAGCCTGGGGCAGGGCCCAGAGTTTCTAATTTACTTCCAAGGCACGGGTGCGGCAGATGACTCAGGGCTGCCCAAAGATCGGTTCTTTGCAGTCAGGCCTGAGGGATCCGTCTCTACTCTGAAGATCCAGCGCACAGAGCAGGGGGACTCAGCCGCGTATCTCCGTGCCAGCAGCTTAAC',
           'GGTGCTGGAGTCTCCCAGACCCCCAGTAACAAGGTCACAGAGAAGGGAAAATATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAAAGCCTGGGGCAGGGCCCAGAGTTTCTAATTTACTTCCAAGGCACGGGTGCGGCAGATGACTCAGGGCTGCCCAACGATCGGTTCTTTGCAGTCAGGCCTGAGGGATCCGTCTCTACTCTGAAGATCCAGCGCACAGAGCGGGGGGACTCTGCCGTGTATCTCTGTGCCAGCAGCTTAAC',
           'GGTGCTGGAGTCTCCCAGTCCCCAAGGTACAAAGTCGCAAAGAGGGGACGGGATGTAGCTCTCAGGTGTGATTCAATTTCGGGTCATGTAACCCTTTATTGGTACCGACAGACCCTGGGGCAGGGCTCAGAGGTTCTGACTTACTCCCAGAGTGATGCTCAACGAGACAAATCAGGGCGGCCCAGTGGTCGGTTCTCTGCAGAGAGGCCTGAGAGATCCGTCTCCACTCTGAAGATCCAGCGCACAGAGCAGGGGGACTCAGCTGTGTATCTCTGTGCCAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGTCTCCCAGGTACAAAGTCACAAAGAGGGGACAGGATGTAGCTCTCAGGTGTGATCCAATTTCGGGTCATGTATCCCTTTATTGGTACCGACAGGCCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCAATTATGAAGCCCAACAAGACAAATCAGGGCTGCCCAATGATCGGTTCTCTGCAGAGAGGCCTGAGGGATCCATCTCCACTCTGACGATCCAGCGCACAGAGCAGCGGGACTCGGCCATGTATCGCTGTGCCAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGTCTCCCAGGTACAAAGTCACAAAGAGGGGACAGGATGTAACTCTCAGGTGTGATCCAATTTCGAGTCATGCAACCCTTTATTGGTATCAACAGGCCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCAATTATGAAGCTCAACCAGACAAATCAGGGCTGCCCAGTGATCGGTTCTCTGCAGAGAGGCCTGAGGGATCCATCTCCACTCTGACGATTCAGCGCACAGAGCAGCGGGACTCAGCCATGTATCGCTGTGCCAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGTCTCCCAGGTACAAAGTCACAAAGAGGGGACAGGATGTAACTCTCAGGTGTGATCCAATTTCGAGTCATGCAACCCTTTATTGGTATCAACAGGCCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCAATTATGAAGCTCAACCAGACAAATCAGGGCTGCCCAGTGATCGGTTCTCTGCAGAGAGGCCTGAGGGATCCATCTCCACTCTGACGATTCAGCGCACAGAGCAGCGGGACTCAGCCATGTATCGCTGTGCTAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGTCCCCTAGGTACAAAGTCGCAAAGAGAGGACAGGATGTAGCTCTCAGGTGTGATCCAATTTCGGGTCATGTATCCCTTTTTTGGTACCAACAGGCCCTGGGGCAGGGGCCAGAGTTTCTGACTTATTTCCAGAATGAAGCTCAACTAGACAAATCGGGGCTGCCCAGTGATCGCTTCTTTGCAGAAAGGCCTGAGGGATCCGTCTCCACTCTGAAGATCCAGCGCACACAGCAGGAGGACTCCGCCGTGTATCTCTGTGCCAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGTCCCCTAGGTACAAAGTCGCAAAGAGAGGACAGGATGTAGCTCTCAGGTGTGATCCAATTTCGGGTCATGTATCCCTTTTTTGGTACCAACAGGCCCTGGGGCAGGGGCCAGAGTTTCTGACTTATTTCCAGAATGAAGCTCAACTAGACAAATCGGGGCTGCCCAGTGATCGCTTCTTTGCAGAAAGGCCTGAGGGATCCGTCTCCACTCTGAAGATCCAGCGCACACAGAAGGAGGACTCCGCCGTGTATCTCTGTGCCAGCAGCTTAGC',
           'GATACTGGAGTCTCCCAGAACCCCAGACACAAGATCACAAAGAGGGGACAGAATGTAACTTTCAGGTGTGATCCAATTTCTGAACACAACCGCCTTTATTGGTACCGACAGACCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCCAGAATGAAGCTCAACTAGAAAAATCAAGGCTGCTCAGTGATCGGTTCTCTGCAGAGAGGCCTAAGGGATCTTTCTCCACCTTGGAGATCCAGCGCACAGAGCAGGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'ATATCTGGAGTCTCCCACAACCCCAGACACAAGATCACAAAGAGGGGACAGAATGTAACTTTCAGGTGTGATCCAATTTCTGAACACAACCGCCTTTATTGGTACCGACAGAACCCTGGGCAGGGCCCAGAGTTTCTGACTTACTTCCAGAATGAAGCTCAACTGGAAAAATCAGGGCTGCTCAGTGATCGGATCTCTGCAGAGAGGCCTAAGGGATCTTTCTCCACCTTGGAGATCCAGCGCACAGAGCAGGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'GATACTGGAGTCTCCCAGAACCCCAGACACAAGATCACAAAGAGGGGACAGAATGTAACTTTCAGGTGTGATCCAATTTCTGAACACAACCGCCTTTATTGGTACCGACAGACCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCCAGAATGAAGCTCAACTAGAAAAATCAAGGCTGCTCAGTGATCGGTTCTCTGCAGAGAGGCCTAAGGGATCTCTCTCCACCTTGGAGATCCAGCGCACAGAGCAGGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'GATACTGGAGTCTCCCAGAACCCCAGACACAAGATCACAAAGAGGGGACAGAATGTAACTTTCAGGTGTGATCCAATTTCTGAACACAACCGCCTTTATTGGTACCGACAGACCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCCAGAATGAAGCTCAACTAGAAAAATCAAGGCTGCTCAGTGATCGGTTCTCTGCAGAGAGGCCTAAGGGATCTCTTTCCACCTTGGAGATCCAGCGCACAGAGCAGGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'CACAACCGCCTTTATTGGTACCGACAGACCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCCAGAATGAAGCTCAACTAGAAAAATCAAGGCTGCTCAGTGATCGGTTCTCTGCAGAGAGGCCTAAGGGATCTTTCTCCACCTTGGAGATCCAGCGCACAGAGGAGGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'GATTCTGGAGTCACACAAACCCCAAAGCACCTGATCACAGCAACTGGACAGCGAGTGACGCTGAGATGCTCCCCTAGGTCTGGAGACCTCTCTGTGTACTGGTACCAACAGAGCCTGGACCAGGGCCTCCAGTTCCTCATTCAGTATTATAATGGAGAAGAGAGAGCAAAAGGAAACATTCTTGAACGATTCTCCGCACAACAGTTCCCTGACTTGCACTCTGAACTAAACCTGAGCTCTCTGGAGCTGGGGGACTCAGCTTTGTATTTCTGTGCCAGCAGCGTAG'],
          dtype=object)

  • j_choice
    (j_choice)
    int64
    0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

    array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14])

  • lbl__j_choice
    (j_choice)
    <U10
    'TRBJ1-1*01' ... 'TRBJ2-7*02'

    array(['TRBJ1-1*01', 'TRBJ1-2*01', 'TRBJ1-3*01', 'TRBJ1-4*01',
           'TRBJ1-5*01', 'TRBJ1-6*01', 'TRBJ1-6*02', 'TRBJ2-1*01',
           'TRBJ2-2*01', 'TRBJ2-3*01', 'TRBJ2-4*01', 'TRBJ2-5*01',
           'TRBJ2-6*01', 'TRBJ2-7*01', 'TRBJ2-7*02'], dtype='<U10')

  • seq__j_choice
    (j_choice)
    object
    'TGAACACTGAAGCTTTCTTTGGACAAGGCAC...

    array(['TGAACACTGAAGCTTTCTTTGGACAAGGCACCAGACTCACAGTTGTAG',
           'CTAACTATGGCTACACCTTCGGTTCGGGGACCAGGTTAACCGTTGTAG',
           'CTCTGGAAACACCATATATTTTGGAGAGGGAAGTTGGCTCACTGTTGTAG',
           'CAACTAATGAAAAACTGTTTTTTGGCAGTGGAACCCAGCTCTCTGTCTTGG',
           'TAGCAATCAGCCCCAGCATTTTGGTGATGGGACTCGACTCTCCATCCTAG',
           'CTCCTATAATTCACCCCTCCACTTTGGGAATGGGACCAGGCTCACTGTGACAG',
           'CTCCTATAATTCACCCCTCCACTTTGGGAACGGGACCAGGCTCACTGTGACAG',
           'CTCCTACAATGAGCAGTTCTTCGGGCCAGGGACACGGCTCACCGTGCTAG',
           'CGAACACCGGGGAGCTGTTTTTTGGAGAAGGCTCTAGGCTGACCGTACTGG',
           'AGCACAGATACGCAGTATTTTGGCCCAGGCACCCGGCTGACAGTGCTCG',
           'AGCCAAAAACATTCAGTACTTCGGCGCCGGGACCCGGCTCTCAGTGCTGG',
           'ACCAAGAGACCCAGTACTTCGGGCCAGGCACGCGGCTCCTGGTGCTCG',
           'CTCTGGGGCCAACGTCCTGACTTTCGGGGCCGGCAGCAGGCTGACCGTGCTGG',
           'CTCCTACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG',
           'CTCCTACGAGCAGTACGTCGGGCCGGGCACCAGGCTCACGGTCACAG'], dtype=object)

• Attributes: (7)

  nickname :

  j_choice

  event_type :

  GeneChoice

  seq_type :

  J_gene

  seq_side :

  Undefined_side

  priority :

  7

  parents :

  ['v_choice']

  childs :

  ['j_5_del', 'd_gene']

P_J_g_V[{'j_choice': 3, 'v_choice': 7}]

<xarray.DataArray ()>
array(0.0052083)
Coordinates:
    v_choice       int64 7
    lbl__v_choice  <U11 'TRBV11-1*01'
    seq__v_choice  object 'GAAGCTGAAGTTGCCCAGTCCCCCAGATATAAGATTACAGAGAAAAGCCA...
    j_choice       int64 3
    lbl__j_choice  <U10 'TRBJ1-4*01'
    seq__j_choice  object 'CAACTAATGAAAAACTGTTTTTTGGCAGTGGAACCCAGCTCTCTGTCTTGG'
Attributes:
    nickname:    j_choice
    event_type:  GeneChoice
    seq_type:    J_gene
    seq_side:    Undefined_side
    priority:    7
    parents:     ['v_choice']
    childs:      ['j_5_del', 'd_gene']

xarray.DataArray

• 0.005208

  array(0.0052083)

• Coordinates: (6)
  • v_choice
    ()
    int64
    7

    array(7)

  • lbl__v_choice
    ()
    <U11
    'TRBV11-1*01'

    array('TRBV11-1*01', dtype='<U11')

  • seq__v_choice
    ()
    object
    'GAAGCTGAAGTTGCCCAGTCCCCCAGATATA...

    array('GAAGCTGAAGTTGCCCAGTCCCCCAGATATAAGATTACAGAGAAAAGCCAGGCTGTGGCTTTTTGGTGTGATCCTATTTCTGGCCATGCTACCCTTTACTGGTACCGGCAGATCCTGGGACAGGGCCCGGAGCTTCTGGTTCAATTTCAGGATGAGAGTGTAGTAGATGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAGCCTGCAGAGCTTGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
          dtype=object)

  • j_choice
    ()
    int64
    3

    array(3)

  • lbl__j_choice
    ()
    <U10
    'TRBJ1-4*01'

    array('TRBJ1-4*01', dtype='<U10')

  • seq__j_choice
    ()
    object
    'CAACTAATGAAAAACTGTTTTTTGGCAGTGG...

    array('CAACTAATGAAAAACTGTTTTTTGGCAGTGGAACCCAGCTCTCTGTCTTGG', dtype=object)

• Attributes: (7)

  nickname :

  j_choice

  event_type :

  GeneChoice

  seq_type :

  J_gene

  seq_side :

  Undefined_side

  priority :

  7

  parents :

  ['v_choice']

  childs :

  ['j_5_del', 'd_gene']

mdl_hb.plot_Event('j_choice')

(<Figure size 1296x1080 with 2 Axes>,
 <AxesSubplot:title={'center':'$P($j_choice$|$v_choice$)$'}, xlabel='j_choice', ylabel='v_choice'>)

Marginal probabilities

Examples of marginals probabilities

$ P(J) = \sum_V P(J|V) P(V) $

$ P(D) = \sum_V P(D|V, J) P(V,J) $

mdl_hb.export_plot_Pmarginals('hb_MP')

mdl_hb.Pmarginal['j_choice']

<xarray.DataArray (j_choice: 15)>
array([0.1196221 , 0.105381  , 0.02016193, 0.05684022, 0.09945699,
       0.03726755, 0.03223616, 0.12542481, 0.05034467, 0.09853413,
       0.0194823 , 0.07500332, 0.01905345, 0.0709004 , 0.07029394])
Coordinates:
  * j_choice       (j_choice) int64 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
    lbl__j_choice  (j_choice) object 'K02545|TRBJ1-1*01|Homo sapiens|F|J-REGI...
    seq__j_choice  (j_choice) object 'TGAACACTGAAGCTTTCTTTGGACAAGGCACCAGACTCA...

xarray.DataArray

• j_choice: 15

• 0.1196 0.1054 0.02016 0.05684 0.09946 ... 0.075 0.01905 0.0709 0.07029

  array([0.1196221 , 0.105381  , 0.02016193, 0.05684022, 0.09945699,
         0.03726755, 0.03223616, 0.12542481, 0.05034467, 0.09853413,
         0.0194823 , 0.07500332, 0.01905345, 0.0709004 , 0.07029394])

• Coordinates: (3)
  • j_choice
    (j_choice)
    int64
    0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

    array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14])

  • lbl__j_choice
    (j_choice)
    object
    'K02545|TRBJ1-1*01|Homo sapiens|...

    array(['K02545|TRBJ1-1*01|Homo sapiens|F|J-REGION|749..796|48 nt|3| | | | |48+0=48| | |',
           'K02545|TRBJ1-2*01|Homo sapiens|F|J-REGION|886..933|48 nt|3| | | | |48+0=48| | |',
           'M14158|TRBJ1-3*01|Homo sapiens|F|J-REGION|1499..1548|50 nt|2| | | | |50+0=50| | |',
           'M14158|TRBJ1-4*01|Homo sapiens|F|J-REGION|2095..2145|51 nt|3| | | | |51+0=51| | |',
           'M14158|TRBJ1-5*01|Homo sapiens|F|J-REGION|2368..2417|50 nt|2| | | | |50+0=50| | |',
           'M14158|TRBJ1-6*01|Homo sapiens|F|J-REGION|2859..2911|53 nt|2| | | | |53+0=53| | |',
           'L36092|TRBJ1-6*02|Homo sapiens|F|J-REGION|643043..643095|53 nt|2| | | | |53+0=53| | |',
           'X02987|TRBJ2-1*01|Homo sapiens|F|J-REGION|800..849|50 nt|2| | | | |50+0=50| | |',
           'X02987|TRBJ2-2*01|Homo sapiens|F|J-REGION|995..1045|51 nt|3| | | | |51+0=51| | |',
           'X02987|TRBJ2-3*01|Homo sapiens|F|J-REGION|1282..1330|49 nt|1| | | | |49+0=49| | |',
           'X02987|TRBJ2-4*01|Homo sapiens|F|J-REGION|1432..1481|50 nt|2| | | | |50+0=50| | |',
           'X02987|TRBJ2-5*01|Homo sapiens|F|J-REGION|1553..1600|48 nt|3| | | | |48+0=48| | |',
           'X02987|TRBJ2-6*01|Homo sapiens|F|J-REGION|1673..1725|53 nt|2| | | | |53+0=53| | |',
           'M14159|TRBJ2-7*01|Homo sapiens|F|J-REGION|2316..2362|47 nt|2| | | | |47+0=47| | |',
           'X02987|TRBJ2-7*02|Homo sapiens|ORF|J-REGION|1890..1936|47 nt|2| | | | |47+0=47| | |'],
          dtype=object)

  • seq__j_choice
    (j_choice)
    object
    'TGAACACTGAAGCTTTCTTTGGACAAGGCAC...

    array(['TGAACACTGAAGCTTTCTTTGGACAAGGCACCAGACTCACAGTTGTAG',
           'CTAACTATGGCTACACCTTCGGTTCGGGGACCAGGTTAACCGTTGTAG',
           'CTCTGGAAACACCATATATTTTGGAGAGGGAAGTTGGCTCACTGTTGTAG',
           'CAACTAATGAAAAACTGTTTTTTGGCAGTGGAACCCAGCTCTCTGTCTTGG',
           'TAGCAATCAGCCCCAGCATTTTGGTGATGGGACTCGACTCTCCATCCTAG',
           'CTCCTATAATTCACCCCTCCACTTTGGGAATGGGACCAGGCTCACTGTGACAG',
           'CTCCTATAATTCACCCCTCCACTTTGGGAACGGGACCAGGCTCACTGTGACAG',
           'CTCCTACAATGAGCAGTTCTTCGGGCCAGGGACACGGCTCACCGTGCTAG',
           'CGAACACCGGGGAGCTGTTTTTTGGAGAAGGCTCTAGGCTGACCGTACTGG',
           'AGCACAGATACGCAGTATTTTGGCCCAGGCACCCGGCTGACAGTGCTCG',
           'AGCCAAAAACATTCAGTACTTCGGCGCCGGGACCCGGCTCTCAGTGCTGG',
           'ACCAAGAGACCCAGTACTTCGGGCCAGGCACGCGGCTCCTGGTGCTCG',
           'CTCTGGGGCCAACGTCCTGACTTTCGGGGCCGGCAGCAGGCTGACCGTGCTGG',
           'CTCCTACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG',
           'CTCCTACGAGCAGTACGTCGGGCCGGGCACCAGGCTCACGGTCACAG'], dtype=object)

• Attributes: (0)

mdl_hb.plot_Event_Marginal('j_choice')

<AxesSubplot:xlabel='j choice', ylabel='P'>

Joint Probabilities

P_V_J = mdl_hb.get_P_joint(['v_choice', 'j_choice'])
P_V_J

<xarray.DataArray (v_choice: 89, j_choice: 15)>
array([[6.28453463e-04, 5.08306114e-04, 2.00831906e-04, ...,
        0.00000000e+00, 2.62143710e-04, 1.82391677e-04],
       [1.54890932e-03, 7.36213918e-04, 1.06011576e-04, ...,
        2.29432410e-04, 6.05154843e-04, 6.95679479e-04],
       [1.54900602e-03, 7.36581450e-04, 1.06039046e-04, ...,
        2.28733827e-04, 6.05348578e-04, 6.95983268e-04],
       ...,
       [4.05407259e-04, 1.55690174e-04, 0.00000000e+00, ...,
        1.15101267e-04, 1.80155267e-04, 1.96566942e-04],
       [3.00565952e-09, 1.68608515e-12, 0.00000000e+00, ...,
        2.81447867e-04, 5.64048061e-05, 6.77364474e-05],
       [1.65903669e-03, 1.77940202e-03, 6.30491475e-04, ...,
        3.45140763e-04, 1.12130116e-03, 9.08844648e-04]])
Coordinates:
  * v_choice       (v_choice) int64 0 1 2 3 4 5 6 7 ... 81 82 83 84 85 86 87 88
    seq__v_choice  (v_choice) object 'GATACTGGAATTACCCAGACACCAAAATACCTGGTCACA...
  * j_choice       (j_choice) int64 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
    seq__j_choice  (j_choice) object 'TGAACACTGAAGCTTTCTTTGGACAAGGCACCAGACTCA...
    lbl__v_choice  (v_choice) <U11 'TRBV1*01' 'TRBV10-1*01' ... 'TRBV9*01'
    lbl__j_choice  (j_choice) <U10 'TRBJ1-1*01' 'TRBJ1-2*01' ... 'TRBJ2-7*02'

xarray.DataArray

• v_choice: 89
• j_choice: 15

• 0.0006285 0.0005083 0.0002008 ... 0.0003451 0.001121 0.0009088

  array([[6.28453463e-04, 5.08306114e-04, 2.00831906e-04, ...,
          0.00000000e+00, 2.62143710e-04, 1.82391677e-04],
         [1.54890932e-03, 7.36213918e-04, 1.06011576e-04, ...,
          2.29432410e-04, 6.05154843e-04, 6.95679479e-04],
         [1.54900602e-03, 7.36581450e-04, 1.06039046e-04, ...,
          2.28733827e-04, 6.05348578e-04, 6.95983268e-04],
         ...,
         [4.05407259e-04, 1.55690174e-04, 0.00000000e+00, ...,
          1.15101267e-04, 1.80155267e-04, 1.96566942e-04],
         [3.00565952e-09, 1.68608515e-12, 0.00000000e+00, ...,
          2.81447867e-04, 5.64048061e-05, 6.77364474e-05],
         [1.65903669e-03, 1.77940202e-03, 6.30491475e-04, ...,
          3.45140763e-04, 1.12130116e-03, 9.08844648e-04]])

• Coordinates: (6)
  • v_choice
    (v_choice)
    int64
    0 1 2 3 4 5 6 ... 83 84 85 86 87 88

    array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16, 17,
           18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
           36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
           54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
           72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88])

  • seq__v_choice
    (v_choice)
    object
    'GATACTGGAATTACCCAGACACCAAAATACC...

    array(['GATACTGGAATTACCCAGACACCAAAATACCTGGTCACAGCAATGGGGAGTAAAAGGACAATGAAACGTGAGCATCTGGGACATGATTCTATGTATTGGTACAGACAGAAAGCTAAGAAATCCCTGGAGTTCATGTTTTACTACAACTGTAAGGAATTCATTGAAAACAAGACTGTGCCAAATCACTTCACACCTGAATGCCCTGACAGCTCTCGCTTATACCTTCATGTGGTCGCACTGCAGCAAGAAGACTCAGCTGCGTATCTCTGCACCAGCAGCCAAGA',
           'GATGCTGAAATCACCCAGAGCCCAAGACACAAGATCACAGAGACAGGAAGGCAGGTGACCTTGGCGTGTCACCAGACTTGGAACCACAACAATATGTTCTGGTATCGACAAGACCTGGGACATGGGCTGAGGCTGATCCATTACTCATATGGTGTTCAAGACACTAACAAAGGAGAAGTCTCAGATGGCTACAGTGTCTCTAGATCAAACACAGAGGACCTCCCCCTCACTCTGGAGTCTGCTGCCTCCTCCCAGACATCTGTATATTTCTGCGCCAGCAGTGAGTC',
           'GATGCTGAAATCACCCAGAGCCCAAGACACAAGATCACAGAGACAGGAAGGCAGGTGACCTTGGCGTGTCACCAGACTTGGAACCACAACAATATGTTCTGGTATCGACAAGACCTGGGACATGGGCTGAGGCTGATCCATTACTCATATGGTGTTCACGACACTAACAAAGGAGAAGTCTCAGATGGCTACAGTGTCTCTAGATCAAACACAGAGGACCTCCCCCTCACTCTGGAGTCTGCTGCCTCCTCCCAGACATCTGTATATTTCTGCGCCAGCAGTGAGTC',
           'GATGCTGAAATCACCCAGAGCCCAAGACACAAGATCACAGAGACAGGAAGGCAGGTGACCTTGGCGTGTCACCAGACTTGGAACCACAACAATATGTTCTGGTATCGACAAGACCTGGGACATGGGCTGAGGCTGATCCATTACTCATATGGTGTTCACGACACTAACAAAGGAGAAGTCTCAGATGGCTACAGTGTCTCTAGATCAAACACAGAGGACCTCCCCCTCACTCTGTAGTCTGCTGCCTCCTCCCAGACATCTGTATATTTCTGCGCCAGCAGTGAGTC',
           'GATGCTGGAATCACCCAGAGCCCAAGATACAAGATCACAGAGACAGGAAGGCAGGTGACCTTGATGTGTCACCAGACTTGGAGCCACAGCTATATGTTCTGGTATCGACAAGACCTGGGACATGGGCTGAGGCTGATCTATTACTCAGCAGCTGCTGATATTACAGATAAAGGAGAAGTCCCCGATGGCTATGTTGTCTCCAGATCCAAGACAGAGAATTTCCCCCTCACTCTGGAGTCAGCTACCCGCTCCCAGACATCTGTGTATTTCTGCGCCAGCAGTGAGTC',
           'GATGCTGGAATCACCCAGAGCCCAAGACACAAGGTCACAGAGACAGGAACACCAGTGACTCTGAGATGTCACCAGACTGAGAACCACCGCTATATGTACTGGTATCGACAAGACCCGGGGCATGGGCTGAGGCTGATCCATTACTCATATGGTGTTAAAGATACTGACAAAGGAGAAGTCTCAGATGGCTATAGTGTCTCTAGATCAAAGACAGAGGATTTCCTCCTCACTCTGGAGTCCGCTACCAGCTCCCAGACATCTGTGTACTTCTGTGCCATCAGTGAGTC',
           'GCTGGAATCACCCAGAGCCCAAGACACAAGGTCACAGAGACAGGAACACCAGTGACTCTGAGATGTCATCAGACTGAGAACCACCGCTATATGTACTGGTATCGACAAGACCCGGGGCATGGGCTGAGGCTGATCCATTACTCATATGGTGTTAAAGATACTGACAAAGGAGAAGTCTCAGATGGCTATAGTGTCTCTAGATCAAAGACAGAGGATTTCCTCCTCACTCTGGAGTCCGCTACCAGCTCCCAGACATCTGTGTACTTCTGTGCCATCAGTGAGTC',
           'GAAGCTGAAGTTGCCCAGTCCCCCAGATATAAGATTACAGAGAAAAGCCAGGCTGTGGCTTTTTGGTGTGATCCTATTTCTGGCCATGCTACCCTTTACTGGTACCGGCAGATCCTGGGACAGGGCCCGGAGCTTCTGGTTCAATTTCAGGATGAGAGTGTAGTAGATGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAGCCTGCAGAGCTTGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'GAAGCTGGAGTTGCCCAGTCTCCCAGATATAAGATTATAGAGAAAAGGCAGAGTGTGGCTTTTTGGTGCAATCCTATATCTGGCCATGCTACCCTTTACTGGTACCAGCAGATCCTGGGACAGGGCCCAAAGCTTCTGATTCAGTTTCAGAATAACGGTGTAGTGGATGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAGCCTGCAAAGCTTGAGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGA',
           'GAAGCTGGAGTTGCCCAGTCTCCCAGATATAAGATTATAGAGAAAAGGCAGAGTGTGGCTTTTTGGTGCAATCCTATATCTGGCCATGCTACCCTTTACTGGTACCAGCAGATCCTGGGACAGGGCCCAAAGCTTCTGATTCAGTTTCAGAATAACGGTGTAGTGGATGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAGCCTGCAAAGCTTGAGAACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGA',
           'GAAGCTGGAGTTGCCCAGTCTCCCAGATATAAGATTATAGAGAAAAGGCAGAGTGTGGCTTTTTGGTGCAATCCTATATCTGGCCATGCTACCCTTTACTGGTACCAGCAGATCCTGGGACAGGGCCCAAAGCTTCTGATTCAGTTTCAGAATAACGGTGTAGTGGATGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAACCTGCAAAGCTTGAGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGA',
           'GAAGCTGGAGTGGTTCAGTCTCCCAGATATAAGATTATAGAGAAAAAACAGCCTGTGGCTTTTTGGTGCAATCCTATTTCTGGCCACAATACCCTTTACTGGTACCTGCAGAACTTGGGACAGGGCCCGGAGCTTCTGATTCGATATGAGAATGAGGAAGCAGTAGACGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAGCCTGCAGAGCTTGGGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGA',
           'GCTGGTGTTATCCAGTCACCCAGGCACAAAGTGACAGAGATGGGACAATCAGTAACTCTGAGATGCGAACCAATTTCAGGCCACAATGATCTTCTCTGGTACAGACAGACCTTTGTGCAGGGACTGGAATTGCTGAATTACTTCTGCAGCTGGACCCTCGTAGATGACTCAGGAGTGTCCAAGGATTGATTCTCAGCACAGATGCCTGATGTATCATTCTCCACTCTGAGGATCCAGCCCATGGAACCCAGGGACTTGGGCCTATATTTCTGTGCCAGCAGCTTTGC',
           'GCTGGCATTATCCAGTCACCCAAGCATGAGGTGACAGAAATGGGACAAACAGTGACTCTGAGATGTGAGCCAATTTTTGGCCACAATTTCCTTTTCTGGTACAGAGATACCTTCGTGCAGGGACTGGAATTGCTGAGTTACTTCCGGAGCTGATCTATTATAGATAATGCAGGTATGCCCACAGAGCGATTCTCAGCTGAGAGGCCTGATGGATCATTCTCTACTCTGAAGATCCAGCCTGCAGAGCAGGGGGACTCGGCCGTGTATGTCTGTGCAAGTCGCTTAGC',
           'GATGCTGGAGTTATCCAGTCACCCCGCCATGAGGTGACAGAGATGGGACAAGAAGTGACTCTGAGATGTAAACCAATTTCAGGCCACAACTCCCTTTTCTGGTACAGACAGACCATGATGCGGGGACTGGAGTTGCTCATTTACTTTAACAACAACGTTCCGATAGATGATTCAGGGATGCCCGAGGATCGATTCTCAGCTAAGATGCCTAATGCATCATTCTCCACTCTGAAGATCCAGCCCTCAGAACCCAGGGACTCAGCTGTGTACTTCTGTGCCAGCAGTTTAGC',
           'GATGCTGGAGTTATCCAGTCACCCCGGCACGAGGTGACAGAGATGGGACAAGAAGTGACTCTGAGATGTAAACCAATTTCAGGACACGACTACCTTTTCTGGTACAGACAGACCATGATGCGGGGACTGGAGTTGCTCATTTACTTTAACAACAACGTTCCGATAGATGATTCAGGGATGCCCGAGGATCGATTCTCAGCTAAGATGCCTAATGCATCATTCTCCACTCTGAAGATCCAGCCCTCAGAACCCAGGGACTCAGCTGTGTACTTCTGTGCCAGCAGTTTAGC',
           'GATGCTGGAGTTATCCAGTCACCCCGGCACGAGGTGACAGAGATGGGACAAGAAGTGACTCTGAGATGTAAACCAATTTCAGGACATGACTACCTTTTCTGGTACAGACAGACCATGATGCGGGGACTGGAGTTGCTCATTTACTTTAACAACAACGTTCCGATAGATGATTCAGGGATGCCCGAGGATCGATTCTCAGCTAAGATGCCTAATGCATCATTCTCCACTCTGAGGATCCAGCCCTCAGAACCCAGGGACTCAGCTGTGTACTTCTGTGCCAGCAGTTTAGC',
           'GATGCTAGAGTCACCCAGACACCAAGGCACAAGGTGACAGAGATGGGACAAGAAGTAACAATGAGATGTCAGCCAATTTTAGGCCACAATACTGTTTTCTGGTACAGACAGACCATGATGCAAGGACTGGAGTTGCTGGCTTACTTCCGCAACCGGGCTCCTCTAGATGATTCGGGGATGCCGAAGGATCGATTCTCAGCAGAGATGCCTGATGCAACTTTAGCCACTCTGAAGATCCAGCCCTCAGAACCCAGGGACTCAGCTGTGTATTTTTGTGCTAGTGGTTTGGT',
           'GCTGCTGGAGTCATCCAGTCCCCAAGACATCTGATCAAAGAAAAGAGGGAAACAGCCACTCTGAAATGCTATCCTATCCCTAGACACGACACTGTCTACTGGTACCAGCAGGGTCCAGGTCAGGACCCCCAGTTCCTCATTTCGTTTTATGAAAAGATGCAGAGCGATAAAGGAAGCATCCCTGATCGATTCTCAGCTCAACAGTTCAGTGACTATCATTCTGAACTGAACATGAGCTCCTTGGAGCTGGGGGACTCAGCCCTGTACTTCTGTGCCAGCAGCTTAGG',
           'GAAGCTGGAGTTACTCAGTTCCCCAGCCACAGCGTAATAGAGAAGGGCCAGACTGTGACTCTGAGATGTGACCCAATTTCTGGACATGATAATCTTTATTGGTATCGACGTGTTATGGGAAAAGAAATAAAATTTCTGTTACATTTTGTGAAAGAGTCTAAACAGGATGAGTCCGGTATGCCCAACAATCGATTCTTAGCTGAAAGGACTGGAGGGACGTATTCTACTCTGAAGGTGCAGCCTGCAGAACTGGAGGATTCTGGAGTTTATTTCTGTGCCAGCAGCCAAGA',
    ...
           'GGAGCTGGAGTCTCCCAGTCCCCCAGTAACAAGGTCACAGAGAAGGGAAAGGATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAGAGGCTGGGGCAGGGCCTGGAGTTTTTAATTTACTTCCAAGGCAACAGTGCACCAGACAAATCAGGGCTGCCCAGTGATCGCTTCTCTGCAGAGAGGACTGGGGAATCCGTCTCCACTCTGACGATCCAGCGCACACAGCAGGAGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGC',
           'GCTGGAGTCTCCCAGTCCCCCAGTAACAAGGTCACAGAGAAGGGAAAGGATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAGAGGCTGGGGCAGGGCCTGGAGTTTTTAATTTACTTCCAAGGCAACAGTGCACCAGACAAATCAGGGCTGCCCAGTGATCGCTTCTCTGCAGAGAGGACTGGGGAATCCGTCTCCACTCTGACGATCCAGCGCACACAGCAGGAGGACTCGGCCGTGTATCTCTGTACCAGCAGCTTAGC',
           'GGAGCTGGAGTCTCCCAGTCCCCCAGTAACAAGGTCACAGAGAAGGGAAAGGATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAGAGGCTGGGGCAGGGCCTGGAGTTTTTAATTTACTTCCAAGGCAACAGTGCACCAGACAAATCAGGGCTGCCCAGTGATCGCTTCTCTGCAGAGAGGACTGGGGAATCCGTCTCCACTCTGACGATCCAGCGCACATAGCAGGAGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGACCCCCAGTAACAAGGTCACAGAGAAGGGAAAATATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAAAGCCTGGGGCAGGGCCCAGAGTTTCTAATTTACTTCCAAGGCACGGGTGCGGCAGATGACTCAGGGCTGCCCAACGATCGGTTCTTTGCAGTCAGGCCTGAGGGATCCGTCTCTACTCTGAAGATCCAGCGCACAGAGCGGGGGGACTCAGCCGTGTATCTCTGTGCCAGCAGCTTAAC',
           'GGTGCTGGAGTCTCCCAGACCCCCAGTAACAAGGTCACAGAGAAGGGAAAAGATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAAAGCCTGGGGCAGGGCCCAGAGTTTCTAATTTACTTCCAAGGCACGGGTGCGGCAGATGACTCAGGGCTGCCCAAAGATCGGTTCTTTGCAGTCAGGCCTGAGGGATCCGTCTCTACTCTGAAGATCCAGCGCACAGAGCAGGGGGACTCAGCCGTGTATCTCCGTGCCAGCAGCTTAAC',
           'GGTGCTGGAGTCTCCCAGACCCCCAGTAACAAGGTCACAGAGAAGGGAAAAGATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAAAGCCTGGGGCAGGGCCCAGAGTTTCTAATTTACTTCCAAGGCACGGGTGCGGCAGATGACTCAGGGCTGCCCAAAGATCGGTTCTTTGCAGTCAGGCCTGAGGGATCCGTCTCTACTCTGAAGATCCAGCGCACAGAGCAGGGGGACTCAGCCGCGTATCTCCGTGCCAGCAGCTTAAC',
           'GGTGCTGGAGTCTCCCAGACCCCCAGTAACAAGGTCACAGAGAAGGGAAAATATGTAGAGCTCAGGTGTGATCCAATTTCAGGTCATACTGCCCTTTACTGGTACCGACAAAGCCTGGGGCAGGGCCCAGAGTTTCTAATTTACTTCCAAGGCACGGGTGCGGCAGATGACTCAGGGCTGCCCAACGATCGGTTCTTTGCAGTCAGGCCTGAGGGATCCGTCTCTACTCTGAAGATCCAGCGCACAGAGCGGGGGGACTCTGCCGTGTATCTCTGTGCCAGCAGCTTAAC',
           'GGTGCTGGAGTCTCCCAGTCCCCAAGGTACAAAGTCGCAAAGAGGGGACGGGATGTAGCTCTCAGGTGTGATTCAATTTCGGGTCATGTAACCCTTTATTGGTACCGACAGACCCTGGGGCAGGGCTCAGAGGTTCTGACTTACTCCCAGAGTGATGCTCAACGAGACAAATCAGGGCGGCCCAGTGGTCGGTTCTCTGCAGAGAGGCCTGAGAGATCCGTCTCCACTCTGAAGATCCAGCGCACAGAGCAGGGGGACTCAGCTGTGTATCTCTGTGCCAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGTCTCCCAGGTACAAAGTCACAAAGAGGGGACAGGATGTAGCTCTCAGGTGTGATCCAATTTCGGGTCATGTATCCCTTTATTGGTACCGACAGGCCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCAATTATGAAGCCCAACAAGACAAATCAGGGCTGCCCAATGATCGGTTCTCTGCAGAGAGGCCTGAGGGATCCATCTCCACTCTGACGATCCAGCGCACAGAGCAGCGGGACTCGGCCATGTATCGCTGTGCCAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGTCTCCCAGGTACAAAGTCACAAAGAGGGGACAGGATGTAACTCTCAGGTGTGATCCAATTTCGAGTCATGCAACCCTTTATTGGTATCAACAGGCCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCAATTATGAAGCTCAACCAGACAAATCAGGGCTGCCCAGTGATCGGTTCTCTGCAGAGAGGCCTGAGGGATCCATCTCCACTCTGACGATTCAGCGCACAGAGCAGCGGGACTCAGCCATGTATCGCTGTGCCAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGTCTCCCAGGTACAAAGTCACAAAGAGGGGACAGGATGTAACTCTCAGGTGTGATCCAATTTCGAGTCATGCAACCCTTTATTGGTATCAACAGGCCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCAATTATGAAGCTCAACCAGACAAATCAGGGCTGCCCAGTGATCGGTTCTCTGCAGAGAGGCCTGAGGGATCCATCTCCACTCTGACGATTCAGCGCACAGAGCAGCGGGACTCAGCCATGTATCGCTGTGCTAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGTCCCCTAGGTACAAAGTCGCAAAGAGAGGACAGGATGTAGCTCTCAGGTGTGATCCAATTTCGGGTCATGTATCCCTTTTTTGGTACCAACAGGCCCTGGGGCAGGGGCCAGAGTTTCTGACTTATTTCCAGAATGAAGCTCAACTAGACAAATCGGGGCTGCCCAGTGATCGCTTCTTTGCAGAAAGGCCTGAGGGATCCGTCTCCACTCTGAAGATCCAGCGCACACAGCAGGAGGACTCCGCCGTGTATCTCTGTGCCAGCAGCTTAGC',
           'GGTGCTGGAGTCTCCCAGTCCCCTAGGTACAAAGTCGCAAAGAGAGGACAGGATGTAGCTCTCAGGTGTGATCCAATTTCGGGTCATGTATCCCTTTTTTGGTACCAACAGGCCCTGGGGCAGGGGCCAGAGTTTCTGACTTATTTCCAGAATGAAGCTCAACTAGACAAATCGGGGCTGCCCAGTGATCGCTTCTTTGCAGAAAGGCCTGAGGGATCCGTCTCCACTCTGAAGATCCAGCGCACACAGAAGGAGGACTCCGCCGTGTATCTCTGTGCCAGCAGCTTAGC',
           'GATACTGGAGTCTCCCAGAACCCCAGACACAAGATCACAAAGAGGGGACAGAATGTAACTTTCAGGTGTGATCCAATTTCTGAACACAACCGCCTTTATTGGTACCGACAGACCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCCAGAATGAAGCTCAACTAGAAAAATCAAGGCTGCTCAGTGATCGGTTCTCTGCAGAGAGGCCTAAGGGATCTTTCTCCACCTTGGAGATCCAGCGCACAGAGCAGGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'ATATCTGGAGTCTCCCACAACCCCAGACACAAGATCACAAAGAGGGGACAGAATGTAACTTTCAGGTGTGATCCAATTTCTGAACACAACCGCCTTTATTGGTACCGACAGAACCCTGGGCAGGGCCCAGAGTTTCTGACTTACTTCCAGAATGAAGCTCAACTGGAAAAATCAGGGCTGCTCAGTGATCGGATCTCTGCAGAGAGGCCTAAGGGATCTTTCTCCACCTTGGAGATCCAGCGCACAGAGCAGGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'GATACTGGAGTCTCCCAGAACCCCAGACACAAGATCACAAAGAGGGGACAGAATGTAACTTTCAGGTGTGATCCAATTTCTGAACACAACCGCCTTTATTGGTACCGACAGACCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCCAGAATGAAGCTCAACTAGAAAAATCAAGGCTGCTCAGTGATCGGTTCTCTGCAGAGAGGCCTAAGGGATCTCTCTCCACCTTGGAGATCCAGCGCACAGAGCAGGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'GATACTGGAGTCTCCCAGAACCCCAGACACAAGATCACAAAGAGGGGACAGAATGTAACTTTCAGGTGTGATCCAATTTCTGAACACAACCGCCTTTATTGGTACCGACAGACCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCCAGAATGAAGCTCAACTAGAAAAATCAAGGCTGCTCAGTGATCGGTTCTCTGCAGAGAGGCCTAAGGGATCTCTTTCCACCTTGGAGATCCAGCGCACAGAGCAGGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'CACAACCGCCTTTATTGGTACCGACAGACCCTGGGGCAGGGCCCAGAGTTTCTGACTTACTTCCAGAATGAAGCTCAACTAGAAAAATCAAGGCTGCTCAGTGATCGGTTCTCTGCAGAGAGGCCTAAGGGATCTTTCTCCACCTTGGAGATCCAGCGCACAGAGGAGGGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTTAGC',
           'GATTCTGGAGTCACACAAACCCCAAAGCACCTGATCACAGCAACTGGACAGCGAGTGACGCTGAGATGCTCCCCTAGGTCTGGAGACCTCTCTGTGTACTGGTACCAACAGAGCCTGGACCAGGGCCTCCAGTTCCTCATTCAGTATTATAATGGAGAAGAGAGAGCAAAAGGAAACATTCTTGAACGATTCTCCGCACAACAGTTCCCTGACTTGCACTCTGAACTAAACCTGAGCTCTCTGGAGCTGGGGGACTCAGCTTTGTATTTCTGTGCCAGCAGCGTAG'],
          dtype=object)

  • j_choice
    (j_choice)
    int64
    0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

    array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14])

  • seq__j_choice
    (j_choice)
    object
    'TGAACACTGAAGCTTTCTTTGGACAAGGCAC...

    array(['TGAACACTGAAGCTTTCTTTGGACAAGGCACCAGACTCACAGTTGTAG',
           'CTAACTATGGCTACACCTTCGGTTCGGGGACCAGGTTAACCGTTGTAG',
           'CTCTGGAAACACCATATATTTTGGAGAGGGAAGTTGGCTCACTGTTGTAG',
           'CAACTAATGAAAAACTGTTTTTTGGCAGTGGAACCCAGCTCTCTGTCTTGG',
           'TAGCAATCAGCCCCAGCATTTTGGTGATGGGACTCGACTCTCCATCCTAG',
           'CTCCTATAATTCACCCCTCCACTTTGGGAATGGGACCAGGCTCACTGTGACAG',
           'CTCCTATAATTCACCCCTCCACTTTGGGAACGGGACCAGGCTCACTGTGACAG',
           'CTCCTACAATGAGCAGTTCTTCGGGCCAGGGACACGGCTCACCGTGCTAG',
           'CGAACACCGGGGAGCTGTTTTTTGGAGAAGGCTCTAGGCTGACCGTACTGG',
           'AGCACAGATACGCAGTATTTTGGCCCAGGCACCCGGCTGACAGTGCTCG',
           'AGCCAAAAACATTCAGTACTTCGGCGCCGGGACCCGGCTCTCAGTGCTGG',
           'ACCAAGAGACCCAGTACTTCGGGCCAGGCACGCGGCTCCTGGTGCTCG',
           'CTCTGGGGCCAACGTCCTGACTTTCGGGGCCGGCAGCAGGCTGACCGTGCTGG',
           'CTCCTACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG',
           'CTCCTACGAGCAGTACGTCGGGCCGGGCACCAGGCTCACGGTCACAG'], dtype=object)

  • lbl__v_choice
    (v_choice)
    <U11
    'TRBV1*01' ... 'TRBV9*01'

    array(['TRBV1*01', 'TRBV10-1*01', 'TRBV10-1*02', 'TRBV10-1*04',
           'TRBV10-2*01', 'TRBV10-3*01', 'TRBV10-3*02', 'TRBV11-1*01',
           'TRBV11-2*01', 'TRBV11-2*02', 'TRBV11-2*03', 'TRBV11-3*01',
           'TRBV12-1*01', 'TRBV12-2*01', 'TRBV12-3*01', 'TRBV12-4*01',
           'TRBV12-4*02', 'TRBV12-5*01', 'TRBV13*01', 'TRBV14*01',
           'TRBV15*01', 'TRBV15*02', 'TRBV15*03', 'TRBV16*01', 'TRBV17*01',
           'TRBV18*01', 'TRBV19*01', 'TRBV2*01', 'TRBV2*03', 'TRBV20-1*01',
           'TRBV23-1*01', 'TRBV24-1*01', 'TRBV25-1*01', 'TRBV26*01',
           'TRBV27*01', 'TRBV28*01', 'TRBV29-1*01', 'TRBV29-1*02',
           'TRBV3-1*01', 'TRBV3-1*02', 'TRBV3-2*01', 'TRBV3-2*02',
           'TRBV30*01', 'TRBV30*02', 'TRBV30*04', 'TRBV4-1*01', 'TRBV4-2*01',
           'TRBV4-3*01', 'TRBV4-3*02', 'TRBV5-1*01', 'TRBV5-3*01',
           'TRBV5-3*02', 'TRBV5-4*01', 'TRBV5-4*02', 'TRBV5-5*01',
           'TRBV5-6*01', 'TRBV5-7*01', 'TRBV5-8*01', 'TRBV6-1*01',
           'TRBV6-2*01', 'TRBV6-3*01', 'TRBV6-4*01', 'TRBV6-5*01',
           'TRBV6-6*01', 'TRBV6-6*02', 'TRBV6-7*01', 'TRBV6-8*01',
           'TRBV6-9*01', 'TRBV7-1*01', 'TRBV7-2*01', 'TRBV7-2*02',
           'TRBV7-2*03', 'TRBV7-2*05', 'TRBV7-3*01', 'TRBV7-3*02',
           'TRBV7-3*03', 'TRBV7-3*04', 'TRBV7-4*01', 'TRBV7-6*01',
           'TRBV7-7*01', 'TRBV7-7*03', 'TRBV7-8*01', 'TRBV7-8*02',
           'TRBV7-9*01', 'TRBV7-9*04', 'TRBV7-9*05', 'TRBV7-9*06',
           'TRBV7-9*07', 'TRBV9*01'], dtype='<U11')

  • lbl__j_choice
    (j_choice)
    <U10
    'TRBJ1-1*01' ... 'TRBJ2-7*02'

    array(['TRBJ1-1*01', 'TRBJ1-2*01', 'TRBJ1-3*01', 'TRBJ1-4*01',
           'TRBJ1-5*01', 'TRBJ1-6*01', 'TRBJ1-6*02', 'TRBJ2-1*01',
           'TRBJ2-2*01', 'TRBJ2-3*01', 'TRBJ2-4*01', 'TRBJ2-5*01',
           'TRBJ2-6*01', 'TRBJ2-7*01', 'TRBJ2-7*02'], dtype='<U10')

• Attributes: (0)

P_V_J.plot(cmap='gnuplot2_r')

<matplotlib.collections.QuadMesh at 0x7f85630c9290>

Entropy

\(H = -P(\vec{E})\sum_{\vec{E}} \log_2 P(\vec{E})\)

mdl_hb.plot_recombination_entropy()

<AxesSubplot:>

mdl_hb.get_df_entropy_decomposition()

	event_nickname	event_type	seq_type	entropy
0	v_choice	GeneChoice	V_gene	5.252905
1	d_gene	GeneChoice	D_gene	1.141779
2	j_choice	GeneChoice	J_gene	3.609102
3	vd_ins	Insertion	VD_genes	14.894931
4	dj_ins	Insertion	DJ_gene	14.981991
5	v_3_del	Deletion	V_gene	3.147511
6	d_3_del	Deletion	D_gene	2.778230
7	d_5_del	Deletion	D_gene	3.634137
8	j_5_del	Deletion	J_gene	3.356340

da_mi = mdl_hb.get_mutual_information()
mdl_hb.plot_mutual_information(da_mi)

<AxesSubplot:>

Evaluate Sequences

str_seq = "TTGAAATGTGAACAACATCTGGGTCATAACGCTATGTATTGGTACAAGCAAAGTGCTAAGAAGCCACTGGAGCTCATGTTTGTCTACAGTCTTGAAGAACGGGTTGAAAACAACAGTGTGCCAAGTCGCTTCTCACCTGAATGCCCCAACAGCTCTCACTTATCCCTTCACCTACACACCCTGCAGCCAGAAGACTCGGCCCTGTATCTCTGCGCCAGCAGCCGTAGGCGAGCGCGGCGGGGAGCTGTTTTTTGGAGAAGGCTCTAGGCTGACCGTACTGG"
str_seq

'TTGAAATGTGAACAACATCTGGGTCATAACGCTATGTATTGGTACAAGCAAAGTGCTAAGAAGCCACTGGAGCTCATGTTTGTCTACAGTCTTGAAGAACGGGTTGAAAACAACAGTGTGCCAAGTCGCTTCTCACCTGAATGCCCCAACAGCTCTCACTTATCCCTTCACCTACACACCCTGCAGCCAGAAGACTCGGCCCTGTATCTCTGCGCCAGCAGCCGTAGGCGAGCGCGGCGGGGAGCTGTTTTTTGGAGAAGGCTCTAGGCTGACCGTACTGG'

df_scens = p3.evaluate(str_seq, mdl_hb, N_scenarios=10, igor_wd='tmp', batch_clean=False)

Writing model parms in file  tmp/dataIGoRrUn7rDfYiq_mdldata/models/model_parms.txt
Writing model marginals in file  tmp/dataIGoRrUn7rDfYiq_mdldata/models/model_marginals.txt
Writing gene anchor's in file  tmp/dataIGoRrUn7rDfYiq_mdldata/ref_genome/V_gene_CDR3_anchors.csv
Writing gene anchor's in file  tmp/dataIGoRrUn7rDfYiq_mdldata/ref_genome/J_gene_CDR3_anchors.csv
Writing model parms in file  tmp/dataIGoRrUn7rDfYiq_mdldata//models/model_parms.txt
Writing model marginals in file  tmp/dataIGoRrUn7rDfYiq_mdldata//models/model_marginals.txt
Writing gene anchor's in file  tmp/dataIGoRrUn7rDfYiq_mdldata//ref_genome/V_gene_CDR3_anchors.csv
Writing gene anchor's in file  tmp/dataIGoRrUn7rDfYiq_mdldata//ref_genome/J_gene_CDR3_anchors.csv
/home/olivares/.local/bin/igor -set_wd tmp -batch dataIGoRrUn7rDfYiq -read_seqs tmp/dataIGoRrUn7rDfYiqinput_sequences.csv
/home/olivares/.local/bin/igor -set_wd tmp -batch dataIGoRrUn7rDfYiq -set_genomic  --V tmp/dataIGoRrUn7rDfYiq_mdldata//ref_genome/genomicVs.fasta --D tmp/dataIGoRrUn7rDfYiq_mdldata//ref_genome/genomicDs.fasta --J tmp/dataIGoRrUn7rDfYiq_mdldata//ref_genome/genomicJs.fasta -set_CDR3_anchors  --V tmp/dataIGoRrUn7rDfYiq_mdldata//ref_genome/V_gene_CDR3_anchors.csv --J tmp/dataIGoRrUn7rDfYiq_mdldata//ref_genome/J_gene_CDR3_anchors.csv -align  --all

Batch name set to: dataIGoRrUn7rDfYiq_
Working directory set to: "tmp/"
Performing V alignments....
V_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing D alignments....
D_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing J alignments....
J_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing CDR3 sequence extraction ....

Writing model parms in file  tmp/dataIGoRrUn7rDfYiq_mdldata//models/model_parms.txt
Writing model marginals in file  tmp/dataIGoRrUn7rDfYiq_mdldata//models/model_marginals.txt
Writing gene anchor's in file  tmp/dataIGoRrUn7rDfYiq_mdldata//ref_genome/V_gene_CDR3_anchors.csv
Writing gene anchor's in file  tmp/dataIGoRrUn7rDfYiq_mdldata//ref_genome/J_gene_CDR3_anchors.csv
/home/olivares/.local/bin/igor -set_wd tmp -batch dataIGoRrUn7rDfYiq -set_custom_model tmp/dataIGoRrUn7rDfYiq_mdldata//models/model_parms.txt tmp/dataIGoRrUn7rDfYiq_mdldata//models/model_marginals.txt -set_CDR3_anchors  --V tmp/dataIGoRrUn7rDfYiq_mdldata//ref_genome/V_gene_CDR3_anchors.csv --J tmp/dataIGoRrUn7rDfYiq_mdldata//ref_genome/J_gene_CDR3_anchors.csv -evaluate  -output  --scenarios 10  --Pgen
igor_fln_generated_realizations_werr:  tmp/dataIGoRrUn7rDfYiq_output/best_scenarios_counts.csv

The column scenario_proba_cond_seq gives us

$ P(\text{scenario}|:nbsphinx-math:sigma) $

and the event columns provide us the selected parameter for the scenarios

$ P(\text{scenario}) = P(\text{v_choice}{id}) :nbsphinx-math:`times `P(:nbsphinx-math:`text{j_choice}`\text{id}|:nbsphinx-math:text{v_choice}{id}) :nbsphinx-math:`times `P(:nbsphinx-math:`text{d_gene}`\text{id} | \text{j_choice}:nbsphinx-math:`text{id}`, :nbsphinx-math:`text{v_choice}`\text{id}) … $

df_scens

	scenario_rank	scenario_proba_cond_seq	v_choice	j_choice	d_gene	v_3_del	d_5_del	j_5_del	d_3_del	vd_ins	vd_dinucl	dj_ins	dj_dinucl	Mismatches	Pgen_estimate
seq_index
0	1	0.178551	48	8	1	8	10	11	10	7	[2, 3, 0, 2, 2, 1, 2]	3	[2, 2, 1]	[]	1.426210e-16
0	2	0.071263	48	8	0	8	9	11	8	2	[2, 3]	9	[2, 2, 1, 2, 1, 2, 0, 2, 1]	[]	1.426210e-16
0	3	0.060515	48	8	0	8	13	11	4	3	[2, 3, 0]	8	[2, 2, 1, 2, 1, 2, 0, 2]	[]	1.426210e-16
0	4	0.042415	48	8	1	8	11	11	9	10	[2, 3, 0, 2, 2, 1, 2, 0, 2, 1]	0	[]	[]	1.426210e-16
0	5	0.038252	48	8	1	8	11	11	10	4	[2, 3, 0, 2]	7	[2, 2, 1, 2, 1, 2, 0]	[]	1.426210e-16
0	6	0.036261	48	8	1	8	11	11	10	8	[2, 3, 0, 2, 2, 1, 2, 0]	3	[2, 2, 1]	[]	1.426210e-16
0	7	0.030704	48	8	2	8	15	11	6	6	[2, 3, 0, 2, 2, 1]	5	[2, 2, 1, 2, 1]	[]	1.426210e-16
0	8	0.028821	48	8	1	8	10	11	11	7	[2, 3, 0, 2, 2, 1, 2]	4	[2, 2, 1, 2]	[]	1.426210e-16
0	9	0.019521	48	8	2	8	16	11	5	2	[2, 3]	9	[2, 2, 1, 2, 1, 2, 0, 2, 1]	[]	1.426210e-16
0	10	0.016049	48	8	0	8	13	11	3	3	[2, 3, 0]	7	[2, 2, 1, 2, 1, 2, 0]	[]	1.426210e-16

Visualize a scenario

ps_scenario = df_scens.iloc[0]
ps_scenario
mdl_hb.plot_scenario(ps_scenario)

<AxesSubplot:>

# ps_scenario = df_scens.iloc[0]
for index, ps_scenario in df_scens.iterrows():
    mdl_hb.plot_scenario(ps_scenario)

mdl_hb.genomic_dataframe_dict['J']

	name	value	anchor_index
id
0	K02545|TRBJ1-1*01|Homo sapiens|F|J-REGION|749....	TGAACACTGAAGCTTTCTTTGGACAAGGCACCAGACTCACAGTTGTAG	17
1	K02545|TRBJ1-2*01|Homo sapiens|F|J-REGION|886....	CTAACTATGGCTACACCTTCGGTTCGGGGACCAGGTTAACCGTTGTAG	17
2	M14158|TRBJ1-3*01|Homo sapiens|F|J-REGION|1499...	CTCTGGAAACACCATATATTTTGGAGAGGGAAGTTGGCTCACTGTT...	19
3	M14158|TRBJ1-4*01|Homo sapiens|F|J-REGION|2095...	CAACTAATGAAAAACTGTTTTTTGGCAGTGGAACCCAGCTCTCTGT...	20
4	M14158|TRBJ1-5*01|Homo sapiens|F|J-REGION|2368...	TAGCAATCAGCCCCAGCATTTTGGTGATGGGACTCGACTCTCCATC...	19
5	M14158|TRBJ1-6*01|Homo sapiens|F|J-REGION|2859...	CTCCTATAATTCACCCCTCCACTTTGGGAATGGGACCAGGCTCACT...	22
6	L36092|TRBJ1-6*02|Homo sapiens|F|J-REGION|6430...	CTCCTATAATTCACCCCTCCACTTTGGGAACGGGACCAGGCTCACT...	22
7	X02987|TRBJ2-1*01|Homo sapiens|F|J-REGION|800....	CTCCTACAATGAGCAGTTCTTCGGGCCAGGGACACGGCTCACCGTG...	19
8	X02987|TRBJ2-2*01|Homo sapiens|F|J-REGION|995....	CGAACACCGGGGAGCTGTTTTTTGGAGAAGGCTCTAGGCTGACCGT...	20
9	X02987|TRBJ2-3*01|Homo sapiens|F|J-REGION|1282...	AGCACAGATACGCAGTATTTTGGCCCAGGCACCCGGCTGACAGTGCTCG	18
10	X02987|TRBJ2-4*01|Homo sapiens|F|J-REGION|1432...	AGCCAAAAACATTCAGTACTTCGGCGCCGGGACCCGGCTCTCAGTG...	19
11	X02987|TRBJ2-5*01|Homo sapiens|F|J-REGION|1553...	ACCAAGAGACCCAGTACTTCGGGCCAGGCACGCGGCTCCTGGTGCTCG	17
12	X02987|TRBJ2-6*01|Homo sapiens|F|J-REGION|1673...	CTCTGGGGCCAACGTCCTGACTTTCGGGGCCGGCAGCAGGCTGACC...	22
13	M14159|TRBJ2-7*01|Homo sapiens|F|J-REGION|2316...	CTCCTACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG	16
14	X02987|TRBJ2-7*02|Homo sapiens|ORF|J-REGION|18...	CTCCTACGAGCAGTACGTCGGGCCGGGCACCAGGCTCACGGTCACAG	16

Generating random sequences from model

df_gen_seqs = p3.generate(Nseqs=10, mdl=mdl_hb)
df_gen_seqs

Writing model parms in file  ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata/models/model_parms.txt
Writing model marginals in file  ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata/models/model_marginals.txt
Writing gene anchor's in file  ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata/ref_genome/V_gene_CDR3_anchors.csv
Writing gene anchor's in file  ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata/ref_genome/J_gene_CDR3_anchors.csv
Writing model parms in file  ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata//models/model_parms.txt
Writing model marginals in file  ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata//models/model_marginals.txt
Writing gene anchor's in file  ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata//ref_genome/V_gene_CDR3_anchors.csv
Writing gene anchor's in file  ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata//ref_genome/J_gene_CDR3_anchors.csv
/home/olivares/.local/bin/igor -set_wd ./igor_generating_u_gmyr0_ -batch dataIGoRdx2C1EIkND -set_custom_model ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata//models/model_parms.txt ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata//models/model_marginals.txt -set_CDR3_anchors  --V ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata//ref_genome/V_gene_CDR3_anchors.csv --J ./igor_generating_u_gmyr0_/dataIGoRdx2C1EIkND_mdldata//ref_genome/J_gene_CDR3_anchors.csv -generate 10

	nt_sequence
seq_index
0	CATGCCAAAGTCACACAGACTCCAGGACATTTGGTCAAAGGAAAAG...
1	GATGCTGGAGTTATCCAGTCACCCCGCCATGAGGTGACAGAGATGG...
2	GGTGCTGTCGTCTCTCAACATCCGAGCTGGGTTATCTGTAAGAGTG...
3	AATGCTGGTGTCACTCAGACCCCAAAATTCCAGGTCCTGAAGACAG...
4	AAGGCTGGAGTCACTCAAACTCCAAGATATCTGATCAAAACGAGAG...
5	AATGCCGGCGTCATGCAGAACCCAAGACACCTGGTCAGGAGGAGGG...
6	GATGCTGATGTTACCCAGACCCCAAGGAATAGGATCACAAAGACAG...
7	AATGCTGGTGTCACTCAGACCCCAAAATTCCGGGTCCTGAAGACAG...
8	GGTGCTGTCGTCTCTCAACATCCGAGCTGGGTTATCTGTAAGAGTG...
9	GACGCTGGAGTCACCCAAAGTCCCACACACCTGATCAAAACGAGAG...

df_gen_seqs = p3.generate(Nseqs=10, mdl=mdl_hb, return_scenarios=True)
df_gen_seqs

Writing model parms in file  ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata/models/model_parms.txt
Writing model marginals in file  ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata/models/model_marginals.txt
Writing gene anchor's in file  ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata/ref_genome/V_gene_CDR3_anchors.csv
Writing gene anchor's in file  ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata/ref_genome/J_gene_CDR3_anchors.csv
Writing model parms in file  ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata//models/model_parms.txt
Writing model marginals in file  ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata//models/model_marginals.txt
Writing gene anchor's in file  ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata//ref_genome/V_gene_CDR3_anchors.csv
Writing gene anchor's in file  ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata//ref_genome/J_gene_CDR3_anchors.csv
/home/olivares/.local/bin/igor -set_wd ./igor_generating_wwkgcy8c -batch dataIGoRWb17vmfBGo -set_custom_model ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata//models/model_parms.txt ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata//models/model_marginals.txt -set_CDR3_anchors  --V ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata//ref_genome/V_gene_CDR3_anchors.csv --J ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_mdldata//ref_genome/J_gene_CDR3_anchors.csv -generate 10
igor_fln_generated_realizations_werr:  ./igor_generating_wwkgcy8c/dataIGoRWb17vmfBGo_generated/generated_realizations_werr.csv

	nt_sequence	v_choice	j_choice	d_gene	v_3_del	d_5_del	j_5_del	d_3_del	vd_ins	vd_dinucl	dj_ins	dj_dinucl	Errors
seq_index
0	GATGGTGGAATCACTCAGTCCCCAAAGTACCTGTTCAGAAAGGAAG...	26	3	0	13	7	9	8	2	[2, 1]	4	[2, 2, 2, 1]	[]
1	ACTGAAGTTACCCAGACACCAAAACACCTGGTCATGGGAATGACAA...	45	9	0	14	6	6	11	11	[3, 2, 1, 0, 0, 1, 1, 1, 1, 2, 2]	7	[1, 3, 2, 3, 0, 2, 2]	[]
2	GGAGCTGGAGTCTCCCAGTCCCCCAGTAACAAGGTCACAGAGAAGG...	70	0	0	11	8	4	9	8	[0, 2, 2, 2, 1, 2, 0, 0]	5	[2, 2, 2, 0, 0]	[]
3	CATGCCAAAGTCACACAGACTCCAGGACATTTGGTCAAAGGAAAAG...	30	3	0	14	3	11	8	4	[0, 0, 0, 2]	9	[2, 0, 1, 3, 1, 0, 0, 2, 2]	[265]
4	GGTGCTGGAGTCTCCCAGACCCCCAGTAACAAGGTCACAGAGAAGG...	73	1	0	9	9	11	7	2	[1, 1]	2	[3, 2]	[]
5	GAGGCTGGAGTCACCCAAAGTCCCACACACCTGATCAAAACGAGAG...	51	10	0	9	9	7	11	6	[2, 1, 1, 0, 2, 3]	0	[]	[]
6	GGTGCTGTCGTCTCTCAACATCCGAGCTGGGTTATCTGTAAGAGTG...	29	4	0	7	4	12	6	3	[3, 1, 1]	11	[3, 3, 3, 0, 1, 1, 1, 1, 2, 3, 2]	[]
7	GAACCTGAAGTCACCCAGACTCCCAGCCATCAGGTCACACAGATGG...	28	9	0	12	13	8	7	7	[0, 1, 1, 3, 2, 1, 0]	0	[]	[]
8	GGTGCTGTCGTCTCTCAACATCCGAGCTGGGTTATCTGTAAGAGTG...	29	7	1	7	4	13	6	3	[3, 1, 3]	4	[2, 3, 3, 2]	[]
9	GGTGCTGTCGTCTCTCAACATCCGAGCTGGGTTATCTGTAAGAGTG...	29	11	0	9	8	6	9	13	[1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 2, 2]	6	[2, 2, 0, 0, 3, 0]	[]

df_gen_seqs['nt_sequence']

seq_index
0    GATGGTGGAATCACTCAGTCCCCAAAGTACCTGTTCAGAAAGGAAG...
1    ACTGAAGTTACCCAGACACCAAAACACCTGGTCATGGGAATGACAA...
2    GGAGCTGGAGTCTCCCAGTCCCCCAGTAACAAGGTCACAGAGAAGG...
3    CATGCCAAAGTCACACAGACTCCAGGACATTTGGTCAAAGGAAAAG...
4    GGTGCTGGAGTCTCCCAGACCCCCAGTAACAAGGTCACAGAGAAGG...
5    GAGGCTGGAGTCACCCAAAGTCCCACACACCTGATCAAAACGAGAG...
6    GGTGCTGTCGTCTCTCAACATCCGAGCTGGGTTATCTGTAAGAGTG...
7    GAACCTGAAGTCACCCAGACTCCCAGCCATCAGGTCACACAGATGG...
8    GGTGCTGTCGTCTCTCAACATCCGAGCTGGGTTATCTGTAAGAGTG...
9    GGTGCTGTCGTCTCTCAACATCCGAGCTGGGTTATCTGTAAGAGTG...
Name: nt_sequence, dtype: object

Inferring a new model

# FIXME: For this example we use some Emerson's data, add the reference

import pandas as pd
df_input = pd.read_csv('HIP00110.tsv.gz', sep='\t')
df_input

	nucleotide	aminoAcid	count (templates/reads)	frequencyCount (%)	cdr3Length	vMaxResolved	vFamilyName	vGeneName	vGeneAllele	vFamilyTies	vGeneNameTies	vGeneAlleleTies	dMaxResolved	dFamilyName	dGeneName	dGeneAllele	dFamilyTies	dGeneNameTies	dGeneAlleleTies	jMaxResolved	jFamilyName	jGeneName	jGeneAllele	jFamilyTies	jGeneNameTies	jGeneAlleleTies	vDeletion	n1Insertion	d5Deletion	d3Deletion	n2Insertion	jDeletion	vIndex	n1Index	dIndex	n2Index	jIndex	estimatedNumberGenomes	sequenceStatus	cloneResolved	vOrphon	dOrphon	jOrphon	vFunction	dFunction	jFunction	fractionNucleated	vAlignLength	vAlignSubstitutionCount	vAlignSubstitutionIndexes	vAlignSubstitutionGeneThreePrimeIndexes	vSeqWithMutations
0	GAATGTGAGCACCTTGGAGCTGGGGGACTCGGCCCTTTATCTTTGC...	NaN	3088	0.019194	38	TCRBV05-01*01	TCRBV05	TCRBV05-01	1.0	NaN	NaN	NaN	TCRBD01-01*01	TCRBD01	TCRBD01-01	1.0	NaN	NaN	NaN	TCRBJ01-06*01	TCRBJ01	TCRBJ01-06	1.0	NaN	NaN	NaN	4	1	5	2	5	10	43	55	60	65	66	3088	Out	VDJ	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
1	GCTACCAGCTCCCAGACATCTGTGTACTTCTGTGCCACCACGGGTA...	CATTGTSGGPSQSTQYF	1772	0.010946	51	TCRBV10-03*01	TCRBV10	TCRBV10-03	1.0	NaN	NaN	NaN	TCRBD02-01*01	TCRBD02	TCRBD02-01	1.0	NaN	NaN	NaN	TCRBJ02-03*01	TCRBJ02	TCRBJ02-03	1.0	NaN	NaN	NaN	10	12	3	2	8	8	30	37	45	56	68	1772	In	VDJ	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
2	ATCCAGCGCACAGAGCAGGGGGACTCGGCCATGTATCTCTGTGCCA...	CASSLRVGGYGYTF	1763	0.010841	42	TCRBV07-09	TCRBV07	TCRBV07-09	NaN	NaN	NaN	01,03	TCRBD02-01*01	TCRBD02	TCRBD02-01	1.0	NaN	NaN	NaN	TCRBJ01-02*01	TCRBJ01	TCRBJ01-02	1.0	NaN	NaN	NaN	2	0	8	2	5	4	39	54	59	-1	65	1763	In	VDJ	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
3	TGCAGCAAGAAGACTCAGCTGCGTATCTCTGCACCAGCAGCCAAGG...	NaN	1241	0.007660	52	TCRBV01-01*01	TCRBV01	TCRBV01-01	1.0	NaN	NaN	NaN	TCRBD02-01*01	TCRBD02	TCRBD02-01	1.0	NaN	NaN	NaN	TCRBJ02-01*01	TCRBJ02	TCRBJ02-01	1.0	NaN	NaN	NaN	1	3	7	1	6	3	29	45	51	59	62	1241	Out	VDJ	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
4	GAGTCTGCCAGGCCCTCACATACCTCTCAGTACCTCTGTGCCAGCA...	CASRRLGGLNTEAFF	985	0.006130	45	TCRBV25-01*01	TCRBV25	TCRBV25-01	1.0	NaN	NaN	NaN	TCRBD02-01*02	TCRBD02	TCRBD02-01	2.0	NaN	NaN	NaN	TCRBJ01-01*01	TCRBJ01	TCRBJ01-01	1.0	NaN	NaN	NaN	6	1	10	0	7	0	36	47	54	60	61	985	In	VDJ	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
130935	AAAAGAACCCGACAGCTTTCTATCTCTGTGCCAGTAACGCGGGTCT...	NaN	1	0.000001	55	TCRBV19-01	TCRBV19	TCRBV19-01	NaN	NaN	NaN	01,02	TCRBD02-01	TCRBD02	TCRBD02-01	NaN	NaN	NaN	01,02	TCRBJ01-05*01	TCRBJ01	TCRBJ01-05	1.0	NaN	NaN	NaN	7	16	7	4	2	0	26	36	38	43	59	1	Out	VDJ	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
130936	AAAAGAACCCGACAGCTTTCTATCTCTGTGCCAGCAGTAACCCCCC...	NaN	1	0.000001	55	TCRBV19-01	TCRBV19	TCRBV19-01	NaN	NaN	NaN	01,02	TCRBD02-01	TCRBD02	TCRBD02-01	NaN	NaN	NaN	01,02	TCRBJ02-04*01	TCRBJ02	TCRBJ02-04	1.0	NaN	NaN	NaN	4	11	8	5	6	0	26	39	45	48	59	1	Out	VDJ	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
130937	AAAACTCATCCTGTACCTTGGAGATCCAGTCCACGGAGTCAGGGGA...	NaN	1	0.000010	19	TCRBV21-01*01	TCRBV21	TCRBV21-01	1.0	NaN	NaN	NaN	NaN	NaN	unresolved	NaN	TCRBD01,TCRBD02	TCRBD01-01,TCRBD02-01	NaN	TCRBJ01-03*01	TCRBJ01	TCRBJ01-03	1.0	NaN	NaN	NaN	20	0	1	8	7	10	62	59	66	-1	69	1	Out	VDJ	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
130938	AAAAAAACAGAATTTCCTGCTGGGGTTGGAGTCGGCTGCTCCCTCC...	NaN	1	0.000002	17	TCRBV06	TCRBV06	unresolved	NaN	NaN	TCRBV06-02,TCRBV06-03	NaN	TCRBD01-01*01	TCRBD01	TCRBD01-01	1.0	NaN	NaN	NaN	TCRBJ02-01*01	TCRBJ02	TCRBJ02-01	1.0	NaN	NaN	NaN	17	0	4	4	0	9	64	-1	64	-1	68	1	Out	VDJ	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
130939	AAAAAAACAGAATTTCCTGCTGGGGTTGGAGTCGGCTGCTCCCTCC...	NaN	1	0.000006	17	TCRBV06	TCRBV06	unresolved	NaN	NaN	TCRBV06-02,TCRBV06-03	NaN	TCRBD01-01*01	TCRBD01	TCRBD01-01	1.0	NaN	NaN	NaN	TCRBJ01-01*01	TCRBJ01	TCRBJ01-01	1.0	NaN	NaN	NaN	18	0	3	4	3	10	64	63	66	-1	71	1	Out	VDJ	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN

130940 rows × 52 columns

Get Genomic Germline templates from IMGT

imgt_species_list = p3.imgt.get_species_list()
print( imgt_species_list )

['', 'Macaca+nemestrina', 'Rattus+norvegicus', 'Mus+saxicola', 'Gallus+gallus', 'Gorilla+gorilla+gorilla', 'Canis+lupus+familiaris', 'Felis+catus', 'Mus+minutoides', 'Salmo+salar', 'Ornithorhynchus+anatinus', 'Oryctolagus+cuniculus', 'Mus+pahari', 'Cercocebus+atys', 'Homo+sapiens', 'Tursiops+truncatus', 'Oncorhynchus+mykiss', 'Papio+anubis+anubis', 'Mus+cookii', 'Heterocephalus+glaber', 'Macaca+mulatta', 'Equus+caballus', 'Bos+taurus', 'Mus+musculus', 'Mustela+putorius+furo', 'Capra+hircus', 'Danio+rerio', 'Sus+scrofa', 'Camelus+dromedarius', 'Ovis+aries', 'Vicugna+pacos', 'Rattus+rattus', 'Macaca+fascicularis', 'Mus+spretus']

imgt_species = 'Homo+sapiens'
imgt_chain = 'TRB'
hb_genomic_dict = p3.imgt.download_ref_genome(imgt_species, imgt_chain, dropna=True)

Homo+sapiens TRBV http://www.imgt.org/genedb/GENElect?query=7.2+TRBV&species=Homo+sapiens
http://www.imgt.org/genedb/GENElect?query=7.2+TRBV&species=Homo+sapiens
Homo+sapiens TRBD http://www.imgt.org/genedb/GENElect?query=7.2+TRBD&species=Homo+sapiens
http://www.imgt.org/genedb/GENElect?query=7.2+TRBD&species=Homo+sapiens
Homo+sapiens TRBJ http://www.imgt.org/genedb/GENElect?query=7.2+TRBJ&species=Homo+sapiens
http://www.imgt.org/genedb/GENElect?query=7.2+TRBJ&species=Homo+sapiens
http://www.imgt.org/genedb/GENElect?query=8.1+TRBV&species=Homo+sapiens&IMGTlabel=2nd-CYS
http://www.imgt.org/genedb/GENElect?query=8.1+TRBJ&species=Homo+sapiens&IMGTlabel=J-PHE
http://www.imgt.org/genedb/GENElect?query=8.1+TRBJ&species=Homo+sapiens&IMGTlabel=J-TRP
http://www.imgt.org/genedb/GENElect?query=8.1+TRBV&species=Homo+sapiens&IMGTlabel=2nd-CYS
http://www.imgt.org/genedb/GENElect?query=8.1+Homo+sapiensJ&species=Homo+sapiens&IMGTlabel=J-PHE
http://www.imgt.org/genedb/GENElect?query=8.1+Homo+sapiensJ&species=Homo+sapiens&IMGTlabel=J-TRP

hb_genomic_dict

{'V':                                                  value         name  \
 0    GATACTGGAATTACCCAGACACCAAAATACCTGGTCACAGCAATGG...     TRBV1*01
 1    GATGCTGAAATCACCCAGAGCCCAAGACACAAGATCACAGAGACAG...  TRBV10-1*01
 2    GATGCTGAAATCACCCAGAGCCCAAGACACAAGATCACAGAGACAG...  TRBV10-1*02
 3    GATGCTGGAATCACCCAGAGCCCAAGATACAAGATCACAGAGACAG...  TRBV10-2*01
 4    GATGCTGGAATCACCCAGAGCCCAAGATACAAGATCACAGAGACAG...  TRBV10-2*02
 ..                                                 ...          ...
 140  GAGGCAGGGATCAGCCAGATACCAAGATATCACAGACACACAGGGA...   TRBV8-1*02
 141  GATGCTGGGATCACCCAGATGCCAAGATATCACATTGTACAGAAGA...   TRBV8-2*02
 142  GATTCTGGAGTCACACAAACCCCAAAGCACCTGATCACAGCAACTG...     TRBV9*01
 143  GATTCTGGAGTCACACAAACCCCAAAGCACCTGATCACAGCAACTG...     TRBV9*02
 144  GATTCTGGAGTCACACAAACCCCAAAGCACCTGATCACAGCAACTG...     TRBV9*03

      anchor_index gfunction
 0             267         P
 1             270         F
 2             270         F
 3             270         F
 4             270         F
 ..            ...       ...
 140           265         P
 141           257         P
 142           270         F
 143           270         F
 144           270       (F)

 [145 rows x 4 columns],
 'D':         name             value
 id
 0   TRBD1*01      GGGACAGGGGGC
 1   TRBD2*01  GGGACTAGCGGGGGGG
 2   TRBD2*02  GGGACTAGCGGGAGGG,
 'J':                                                 value        name  \
 0    TGAACACTGAAGCTTTCTTTGGACAAGGCACCAGACTCACAGTTGTAG  TRBJ1-1*01
 1    CTAACTATGGCTACACCTTCGGTTCGGGGACCAGGTTAACCGTTGTAG  TRBJ1-2*01
 2   CTCTGGAAACACCATATATTTTGGAGAGGGAAGTTGGCTCACTGTT...  TRBJ1-3*01
 3   CAACTAATGAAAAACTGTTTTTTGGCAGTGGAACCCAGCTCTCTGT...  TRBJ1-4*01
 4   TAGCAATCAGCCCCAGCATTTTGGTGATGGGACTCGACTCTCCATC...  TRBJ1-5*01
 5   CTCCTATAATTCACCCCTCCACTTTGGGAATGGGACCAGGCTCACT...  TRBJ1-6*01
 6   CTCCTATAATTCACCCCTCCACTTTGGGAACGGGACCAGGCTCACT...  TRBJ1-6*02
 7   CTCCTACAATGAGCAGTTCTTCGGGCCAGGGACACGGCTCACCGTG...  TRBJ2-1*01
 8   CGAACACCGGGGAGCTGTTTTTTGGAGAAGGCTCTAGGCTGACCGT...  TRBJ2-2*01
 9   AGCACAGATACGCAGTATTTTGGCCCAGGCACCCGGCTGACAGTGCTCG  TRBJ2-3*01
 10  AGCCAAAAACATTCAGTACTTCGGCGCCGGGACCCGGCTCTCAGTG...  TRBJ2-4*01
 11   ACCAAGAGACCCAGTACTTCGGGCCAGGCACGCGGCTCCTGGTGCTCG  TRBJ2-5*01
 12  CTCTGGGGCCAACGTCCTGACTTTCGGGGCCGGCAGCAGGCTGACC...  TRBJ2-6*01
 13    CTCCTACGAGCAGTACTTCGGGCCGGGCACCAGGCTCACGGTCACAG  TRBJ2-7*01

     anchor_index function
 0             17        F
 1             17        F
 2             19        F
 3             20        F
 4             19        F
 5             22        F
 6             22        F
 7             19        F
 8             20        F
 9             18        F
 10            19        F
 11            17        F
 12            22        F
 13            16        F  }

Create a new model

hb_mdl_0 = p3.IgorModel.make_default_from_Dataframe_dict(hb_genomic_dict)

df_input_test = df_input['nucleotide'].loc[:500]
df_input_test

0      GAATGTGAGCACCTTGGAGCTGGGGGACTCGGCCCTTTATCTTTGC...
1      GCTACCAGCTCCCAGACATCTGTGTACTTCTGTGCCACCACGGGTA...
2      ATCCAGCGCACAGAGCAGGGGGACTCGGCCATGTATCTCTGTGCCA...
3      TGCAGCAAGAAGACTCAGCTGCGTATCTCTGCACCAGCAGCCAAGG...
4      GAGTCTGCCAGGCCCTCACATACCTCTCAGTACCTCTGTGCCAGCA...
                             ...
496    CTGGAGCTGGGGGACTCAGCTTTGTATTTCTGTGCCAGCAGCGTAA...
497    CTGCTGTCGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCA...
498    CTGCTGTCGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCA...
499    CTGAAGATCCGGTCCACAAAGCTGGAGGACTCAGCCATGTACTTCT...
500    CTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTGGGACTA...
Name: nucleotide, Length: 501, dtype: object

df_functionality, df_CDR3 = p3.naive_align(df_input_test, hb_mdl_0)

Writing model parms in file  ./igor_aligning_3_y3t_de/dataIGoRfD02VCeWdL_mdldata/models/model_parms.txt
Writing model marginals in file  ./igor_aligning_3_y3t_de/dataIGoRfD02VCeWdL_mdldata/models/model_marginals.txt
/home/olivares/.local/bin/igor -set_wd ./igor_aligning_3_y3t_de -batch dataIGoRfD02VCeWdL -read_seqs ./igor_aligning_3_y3t_de/dataIGoRfD02VCeWdLinput_sequences.csv
/home/olivares/.local/bin/igor -set_wd ./igor_aligning_3_y3t_de -batch dataIGoRfD02VCeWdL -set_genomic  --V ./igor_aligning_3_y3t_de/dataIGoRfD02VCeWdL_mdldata/ref_genome/genomicVs.fasta --D ./igor_aligning_3_y3t_de/dataIGoRfD02VCeWdL_mdldata/ref_genome/genomicDs.fasta --J ./igor_aligning_3_y3t_de/dataIGoRfD02VCeWdL_mdldata/ref_genome/genomicJs.fasta -set_CDR3_anchors  --V ./igor_aligning_3_y3t_de/dataIGoRfD02VCeWdL_mdldata/ref_genome/V_gene_CDR3_anchors.csv --J ./igor_aligning_3_y3t_de/dataIGoRfD02VCeWdL_mdldata/ref_genome/J_gene_CDR3_anchors.csv -align  --all   ---best_align_only true

Batch name set to: dataIGoRfD02VCeWdL_
Working directory set to: "./igor_aligning_3_y3t_de/"
Performing V alignments....
V_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing D alignments....
D_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing J alignments....
J_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing CDR3 sequence extraction ....

df_functionality

	functionality	in_frame	stop_codon
seq_index
0	False	False	True
1	True	True	False
2	True	True	False
3	False	False	True
4	True	True	False
...	...	...	...
496	True	True	False
497	True	True	False
498	True	True	False
499	True	True	False
500	False	False	True

501 rows × 3 columns

df_CDR3

	v_anchor	j_anchor	CDR3nt	CDR3aa	v_call	j_call
seq_index
0	43.0	81.0	TGCGCCAGCAGCATCAAAGGGGCTCACCCCTCCACTTT	NaN	TRBV5-1*01	TRBJ1-6*02
1	30.0	81.0	TGTGCCACCACGGGTACTAGCGGGGGCCCAAGCCAGAGTACGCAGT...	CATTGTSGGPSQSTQYF	TRBV10-3*01	TRBJ2-3*01
2	39.0	81.0	TGTGCCAGCAGCTTACGAGTCGGGGGCTATGGCTACACCTTC	CASSLRVGGYGYTF	TRBV7-9*01	TRBJ1-2*01
3	29.0	81.0	TGCACCAGCAGCCAAGGGGATCGCGGGGGGCCACTACAATGAGCAG...	NaN	TRBV1*01	TRBJ2-1*01
4	36.0	81.0	TGTGCCAGCAGACGCCTCGGAGGGTTGAACACTGAAGCTTTCTTT	CASRRLGGLNTEAFF	TRBV25-1*01	TRBJ1-1*01
...	...	...	...	...	...	...
496	30.0	81.0	TGTGCCAGCAGCGTAAGGGGGACTAGCGGGGGGTCCGCTACGCAGT...	CASSVRGTSGGSATQYF	TRBV9*01	TRBJ2-3*01
497	39.0	81.0	TGTGCCAGCAGTTATATCCCTGTCAGGGAAGAGCAGTACTTC	CASSYIPVREEQYF	TRBV6-5*01	TRBJ2-7*01
498	39.0	81.0	TGTGCCAGCAGGCAGGGGGCGCGAGGAAACACCATATATTTT	CASRQGARGNTIYF	TRBV6-5*01	TRBJ1-3*01
499	45.0	81.0	TGTGCCAGCAGTTTCCGCCCCTATGAGCAGTTCTTC	CASSFRPYEQFF	TRBV2*01	TRBJ2-1*01
500	26.0	81.0	TGTGCCAGCAGTTGGGACTAGCGGGGATTTGAGCTCCTACAATGAG...	NaN	TRBV6-5*01	TRBJ2-1*01

501 rows × 6 columns

df_input_test_no_productive = df_input_test.loc[~df_functionality['functionality'] ]
df_input_test_no_productive

0      GAATGTGAGCACCTTGGAGCTGGGGGACTCGGCCCTTTATCTTTGC...
3      TGCAGCAAGAAGACTCAGCTGCGTATCTCTGCACCAGCAGCCAAGG...
8      ATCCAGCGCACAGAGCAGGGGGACTCGGCCATGTATCTCTGTGCCA...
9      GGCTGCTGTCGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGC...
12     ACCTACACGCCCTGCAGCCAGAAGACTCAGCCCTGTATCTCTGCGC...
                             ...
487    GAGCTCTCTGGAGCTGGGGGACTCAGCTTTGTATTTCTGTGCCAGA...
488    GAGCACCTTGGAGCTGGGGGACTCGGCCCTTTATCTTTGCGCCAGC...
489    GAGCAACATGAGCCCTGAAGACAGCAGCATATATCTCTGCAGCGTC...
490    CTTGGAGCTGGAGGACTCGGCCCTGTATCTCTGTGCCAGCATCCTG...
500    CTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTGGGACTA...
Name: nucleotide, Length: 105, dtype: object

hb_mdl_new, df_likelihoods = p3.infer(df_input_test_no_productive, hb_mdl_0, N_iter=10, return_likelihoods=True)

Writing model parms in file  ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata/models/model_parms.txt
Writing model marginals in file  ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata/models/model_marginals.txt
/home/olivares/.local/bin/igor -set_wd ./igor_inferring_8stxm4z4 -batch dataIGoR1hwusR6KOG -read_seqs ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOGinput_sequences.csv
/home/olivares/.local/bin/igor -set_wd ./igor_inferring_8stxm4z4 -batch dataIGoR1hwusR6KOG -set_genomic  --V ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata/ref_genome/genomicVs.fasta --D ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata/ref_genome/genomicDs.fasta --J ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata/ref_genome/genomicJs.fasta -set_CDR3_anchors  --V ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata/ref_genome/V_gene_CDR3_anchors.csv --J ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata/ref_genome/J_gene_CDR3_anchors.csv -align  --all

Batch name set to: dataIGoR1hwusR6KOG_
Working directory set to: "./igor_inferring_8stxm4z4/"
Performing V alignments....
V_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing D alignments....
D_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing J alignments....
J_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing CDR3 sequence extraction ....
Batch name set to: dataIGoR1hwusR6KOG_
GeneChoice read
GeneChoice read
GeneChoice read
Deletion read
Deletion read
Deletion read
Deletion read
Insertion read
DinucMarkov read
Insertion read
DinucMarkov read
Working directory set to: "./igor_inferring_8stxm4z4/"
Performing Evaluate/Inference iteration 1
Initializing probability bounds...

== Alignment finished! ==
Writing model parms in file  ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata//models/model_parms.txt
Writing model marginals in file  ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata//models/model_marginals.txt
/home/olivares/.local/bin/igor -set_wd ./igor_inferring_8stxm4z4 -batch dataIGoR1hwusR6KOG -set_custom_model ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata//models/model_parms.txt ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata//models/model_marginals.txt -set_CDR3_anchors  --V ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata//ref_genome/V_gene_CDR3_anchors.csv --J ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_mdldata//ref_genome/J_gene_CDR3_anchors.csv -infer   --N_iter 10

Initialization of probability bounds over.
Iteration 1 [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing Evaluate/Inference iteration 2
Initializing probability bounds...
Initialization of probability bounds over.
Iteration 2 [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing Evaluate/Inference iteration 3
Initializing probability bounds...
Initialization of probability bounds over.
Iteration 3 [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing Evaluate/Inference iteration 4
Initializing probability bounds...
Initialization of probability bounds over.
Iteration 4 [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing Evaluate/Inference iteration 5
Initializing probability bounds...
Initialization of probability bounds over.
Iteration 5 [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing Evaluate/Inference iteration 6
Initializing probability bounds...
Initialization of probability bounds over.
Iteration 6 [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing Evaluate/Inference iteration 7
Initializing probability bounds...
Initialization of probability bounds over.
Iteration 7 [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing Evaluate/Inference iteration 8
Initializing probability bounds...
Initialization of probability bounds over.
Iteration 8 [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing Evaluate/Inference iteration 9
Initializing probability bounds...
Initialization of probability bounds over.
Iteration 9 [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.
Performing Evaluate/Inference iteration 10
Initializing probability bounds...
Initialization of probability bounds over.
Iteration 10 [||||||||||||||||||||||||||||||||||||||||||||||||||]  Done.

Reading Parms filename from:  ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_inference/final_parms.txt
Reading Marginals filename from:  ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_inference/final_marginals.txt
Reading Parms filename from:  ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_inference/final_parms.txt
Reading Marginals filename from:  ./igor_inferring_8stxm4z4/dataIGoR1hwusR6KOG_inference/final_marginals.txt

df_likelihoods

	iteration	mean_log_Likelihood	n_seq
0	1	-16.0033	104
1	2	-11.6762	104
2	3	-11.3408	104
3	4	-11.1774	104
4	5	-11.0885	104
5	6	-11.0380	104
6	7	-11.0009	104
7	8	-10.9747	104
8	9	-10.9552	104
9	10	-10.9353	104

df_likelihoods['mean_log_Likelihood'].plot()

<AxesSubplot:>

hb_mdl_new.export_plot_Pconditionals('CP_hb_new')