Welcome to abbert2 đź‘‹, a library to enable training of machine learning models over large repertoires of antibodies.
abbert2 is young and under heavy development, so expect rough edges
# clone the repo
git clone https://github.com/bayer-science-for-a-better-life/abbert-cerebras.git abbert2
cd abbert2
# create the conda environment
conda env create -f environment.yml
# activate it
conda activate abbert2
# if everything worked well, this should work
# it is a small example of how to access the preprocessed data dumps from OAS
python examples/oas101.pyClick to see the expected output!
UNIT: ('paired', 'Setliff_2019', 'SRR10313335_paired')
{'age': 'no',
'bsource': 'PBMC',
'btype': 'Unsorted-B-Cells',
'chain': 'Paired',
'disease': 'HIV',
'download_date': Timestamp('2021-09-19 03:56:33+0000', tz='UTC'),
'download_error': None,
'has_original_csv': False,
'heavy_cdr3_max_length': 25,
'isotype': 'All',
'longitudinal': 'Year-23',
'needs_redownload': True,
'oas_subset': 'paired',
'online_csv_size_bytes': 1510324,
'online_modified_date': Timestamp('2021-07-31 13:44:00+0000', tz='UTC'),
'original_local_csv_mdate': None,
'original_url': 'http://opig.stats.ox.ac.uk/webapps/ngsdb/paired/Setliff_2019/csv/SRR10313335_paired.csv.gz',
'publication_link': 'https://doi.org/10.1016/j.cell.2019.11.003',
'sequences_file_size': 73103,
'sequences_miss_processing': True,
'sequences_num_records': 100,
'sequencing_run': 'SRR10313335',
'species': 'human',
'study_author': 'Setliff et al., 2019',
'study_id': 'Setliff_2019',
'subject': 'Donor-N90',
'theoretical_num_sequences_total': None,
'theoretical_num_sequences_unique': 1444,
'unit_id': 'SRR10313335_paired',
'vaccine': 'None'}
Unit disease=HIV, vaccine=None
<class 'pandas.core.frame.DataFrame'>
Int64Index: 100 entries, 1399 to 1190
Data columns (total 76 columns):
# Column Non-Null Count Dtype
--- ------ -------------- -----
0 locus_heavy 100 non-null object
1 locus_light 100 non-null object
2 stop_codon_heavy 100 non-null object
3 stop_codon_light 100 non-null object
4 vj_in_frame_heavy 100 non-null object
5 vj_in_frame_light 100 non-null object
6 productive_heavy 100 non-null object
7 productive_light 100 non-null object
8 rev_comp_heavy 100 non-null object
9 rev_comp_light 100 non-null object
10 v_call_heavy 100 non-null object
11 v_call_light 100 non-null object
12 d_call_heavy 99 non-null object
13 d_call_light 0 non-null float64
14 j_call_heavy 100 non-null object
15 j_call_light 100 non-null object
16 junction_aa_heavy 100 non-null object
17 junction_aa_light 100 non-null object
18 junction_aa_length_heavy 100 non-null UInt16
19 junction_aa_length_light 100 non-null UInt16
20 anarci_status_heavy 100 non-null object
21 anarci_status_light 100 non-null object
22 unfit_heavy 100 non-null bool
23 has_unexpected_insertions_heavy 100 non-null bool
24 has_mutated_conserved_cysteines_heavy 100 non-null bool
25 has_wrong_sequence_reconstruction_heavy 0 non-null object
26 has_wrong_cdr3_reconstruction_heavy 100 non-null bool
27 has_kappa_gap_21_heavy 100 non-null bool
28 has_long_cdr1_heavy 100 non-null bool
29 has_long_cdr2_heavy 100 non-null bool
30 has_long_cdr3_heavy 100 non-null bool
31 has_insertions_heavy 100 non-null bool
32 fw1_start_heavy 100 non-null int64
33 fw1_length_heavy 100 non-null int64
34 cdr1_start_heavy 100 non-null int64
35 cdr1_length_heavy 100 non-null int64
36 fw2_start_heavy 100 non-null int64
37 fw2_length_heavy 100 non-null int64
38 cdr2_start_heavy 100 non-null int64
39 fw3_start_heavy 100 non-null int64
40 fw3_length_heavy 100 non-null int64
41 cdr2_length_heavy 100 non-null int64
42 cdr3_start_heavy 100 non-null int64
43 cdr3_length_heavy 100 non-null int64
44 fw4_start_heavy 100 non-null int64
45 fw4_length_heavy 100 non-null int64
46 aligned_sequence_heavy 100 non-null object
47 positions_heavy 100 non-null object
48 insertions_heavy 80 non-null object
49 unfit_light 100 non-null bool
50 has_unexpected_insertions_light 100 non-null bool
51 has_mutated_conserved_cysteines_light 100 non-null bool
52 has_wrong_sequence_reconstruction_light 0 non-null object
53 has_wrong_cdr3_reconstruction_light 100 non-null bool
54 has_kappa_gap_21_light 100 non-null bool
55 has_long_cdr1_light 100 non-null bool
56 has_long_cdr2_light 100 non-null bool
57 has_long_cdr3_light 100 non-null bool
58 has_insertions_light 100 non-null bool
59 fw1_start_light 100 non-null int64
60 fw1_length_light 100 non-null int64
61 cdr1_start_light 100 non-null int64
62 cdr1_length_light 100 non-null int64
63 fw2_start_light 100 non-null int64
64 fw2_length_light 100 non-null int64
65 cdr2_start_light 100 non-null int64
66 fw3_start_light 100 non-null int64
67 fw3_length_light 100 non-null int64
68 cdr2_length_light 100 non-null int64
69 cdr3_start_light 100 non-null int64
70 cdr3_length_light 100 non-null int64
71 fw4_start_light 100 non-null int64
72 fw4_length_light 100 non-null int64
73 aligned_sequence_light 100 non-null object
74 positions_light 100 non-null object
75 insertions_light 0 non-null object
dtypes: UInt16(2), bool(18), float64(1), int64(28), object(27)
memory usage: 46.9+ KB
An antibody light chain: [b'E' b'I' b'V' b'M' b'T' b'Q' b'S' b'P' b'A' b'T' b'L' b'S' b'V' b'S'
b'P' b'G' b'E' b'R' b'A' b'T' b'L' b'S' b'C' b'R' b'A' b'S' b'Q' b'S'
b'V' b'S' b'S' b'N' b'L' b'A' b'W' b'Y' b'Q' b'Q' b'K' b'P' b'G' b'Q'
b'A' b'P' b'R' b'L' b'L' b'I' b'Y' b'G' b'A' b'S' b'T' b'R' b'A' b'T'
b'G' b'I' b'P' b'A' b'R' b'F' b'S' b'G' b'S' b'G' b'S' b'G' b'T' b'E'
b'F' b'T' b'L' b'T' b'I' b'S' b'S' b'L' b'Q' b'S' b'E' b'D' b'F' b'A'
b'V' b'Y' b'Y' b'C' b'Q' b'Q' b'Y' b'N' b'N' b'W' b'P' b'P' b'L' b'T'
b'F' b'G' b'G' b'G' b'T' b'K' b'V' b'E' b'I' b'K']
An antibody heavy chain: [b'E' b'V' b'Q' b'L' b'V' b'E' b'S' b'G' b'G' b'G' b'L' b'V' b'K' b'P'
b'G' b'G' b'S' b'L' b'R' b'L' b'S' b'C' b'A' b'A' b'S' b'A' b'F' b'T'
b'F' b'S' b'N' b'A' b'W' b'M' b'S' b'W' b'V' b'R' b'Q' b'A' b'P' b'G'
b'K' b'G' b'L' b'E' b'W' b'V' b'G' b'L' b'I' b'K' b'S' b'K' b'S' b'D'
b'G' b'G' b'T' b'A' b'D' b'Y' b'A' b'A' b'P' b'V' b'K' b'G' b'R' b'F'
b'T' b'I' b'S' b'R' b'D' b'D' b'S' b'K' b'N' b'T' b'L' b'F' b'L' b'Q'
b'M' b'N' b'S' b'L' b'K' b'S' b'E' b'D' b'T' b'A' b'V' b'Y' b'Y' b'C'
b'T' b'T' b'R' b'L' b'D' b'Y' b'S' b'D' b'Y' b'F' b'F' b'Y' b'H' b'Y'
b'Y' b'F' b'M' b'D' b'V' b'W' b'G' b'K' b'G' b'T' b'T' b'V' b'T' b'V'
b'S' b'S']
--------------------------------------------------------------------------------
UNIT: ('unpaired', 'Bhiman_2015', 'SRR2126755_Heavy_IGHM')
{'age': 'no',
'bsource': 'PBMC',
'btype': 'Unsorted-B-Cells',
'chain': 'Heavy',
'disease': 'HIV',
'download_date': Timestamp('2021-09-19 03:56:43+0000', tz='UTC'),
'download_error': None,
'has_original_csv': False,
'heavy_cdr3_max_length': 16,
'isotype': 'IGHM',
'longitudinal': 'no',
'needs_redownload': True,
'oas_subset': 'unpaired',
'online_csv_size_bytes': 2469,
'online_modified_date': Timestamp('2021-08-09 16:10:00+0000', tz='UTC'),
'original_local_csv_mdate': None,
'original_url': 'http://opig.stats.ox.ac.uk/webapps/ngsdb/unpaired/Bhiman_2015/csv/SRR2126755_Heavy_IGHM.csv.gz',
'publication_link': 'https://doi.org/10.1038/nm.3963',
'sequences_file_size': 31089,
'sequences_miss_processing': False,
'sequences_num_records': 2,
'sequencing_run': 'SRR2126755',
'species': 'human',
'study_author': 'Bhiman et al., 2015',
'study_id': 'Bhiman_2015',
'subject': 'CAP256',
'theoretical_num_sequences_total': 2,
'theoretical_num_sequences_unique': 2,
'unit_id': 'SRR2126755_Heavy_IGHM',
'vaccine': 'None'}
Unit disease=HIV, vaccine=None
<class 'pandas.core.frame.DataFrame'>
Int64Index: 2 entries, 0 to 1
Data columns (total 41 columns):
# Column Non-Null Count Dtype
--- ------ -------------- -----
0 locus_heavy 2 non-null object
1 stop_codon_heavy 2 non-null object
2 vj_in_frame_heavy 2 non-null object
3 v_frameshift_heavy 2 non-null object
4 productive_heavy 2 non-null object
5 rev_comp_heavy 2 non-null object
6 complete_vdj_heavy 2 non-null object
7 v_call_heavy 2 non-null object
8 d_call_heavy 2 non-null object
9 j_call_heavy 2 non-null object
10 junction_aa_heavy 2 non-null object
11 junction_aa_length_heavy 2 non-null UInt16
12 redundancy_heavy 2 non-null int64
13 anarci_status_heavy 2 non-null object
14 unfit_heavy 2 non-null bool
15 has_unexpected_insertions_heavy 2 non-null bool
16 has_mutated_conserved_cysteines_heavy 2 non-null bool
17 has_wrong_sequence_reconstruction_heavy 0 non-null object
18 has_wrong_cdr3_reconstruction_heavy 2 non-null bool
19 has_kappa_gap_21_heavy 2 non-null bool
20 has_long_cdr1_heavy 2 non-null bool
21 has_long_cdr2_heavy 2 non-null bool
22 has_long_cdr3_heavy 2 non-null bool
23 has_insertions_heavy 2 non-null bool
24 fw1_start_heavy 2 non-null int64
25 fw1_length_heavy 2 non-null int64
26 cdr1_start_heavy 2 non-null int64
27 cdr1_length_heavy 2 non-null int64
28 fw2_start_heavy 2 non-null int64
29 fw2_length_heavy 2 non-null int64
30 cdr2_start_heavy 2 non-null int64
31 fw3_start_heavy 2 non-null int64
32 fw3_length_heavy 2 non-null int64
33 cdr2_length_heavy 2 non-null int64
34 cdr3_start_heavy 2 non-null int64
35 cdr3_length_heavy 2 non-null int64
36 fw4_start_heavy 2 non-null int64
37 fw4_length_heavy 2 non-null int64
38 aligned_sequence_heavy 2 non-null object
39 positions_heavy 2 non-null object
40 insertions_heavy 2 non-null object
dtypes: UInt16(1), bool(9), int64(15), object(16)
memory usage: 536.0+ bytes
An antibody heavy chain: [b'E' b'V' b'Q' b'L' b'V' b'E' b'S' b'G' b'G' b'G' b'L' b'V' b'Q' b'P'
b'G' b'G' b'S' b'L' b'R' b'L' b'S' b'C' b'A' b'A' b'S' b'G' b'F' b'T'
b'F' b'S' b'T' b'Y' b'D' b'M' b'H' b'W' b'V' b'R' b'Q' b'G' b'A' b'G'
b'K' b'G' b'P' b'E' b'W' b'V' b'A' b'G' b'I' b'G' b'R' b'A' b'G' b'D'
b'T' b'Y' b'Y' b'P' b'G' b'S' b'E' b'K' b'G' b'R' b'F' b'T' b'I' b'S'
b'R' b'E' b'N' b'A' b'K' b'N' b'S' b'L' b'Y' b'L' b'E' b'M' b'N' b'S'
b'L' b'R' b'A' b'G' b'D' b'T' b'A' b'V' b'Y' b'Y' b'C' b'A' b'R' b'R'
b'R' b'Q' b'G' b'S' b'A' b'S' b'Y' b'S' b'D' b'A' b'F' b'D' b'I' b'W'
b'G' b'Q' b'G' b'T' b'M' b'V' b'T' b'V' b'S' b'S']
--------------------------------------------------------------------------------The Observed Antibody Space (OAS) data is licensed under a CC-BY 4.0 license.