Add Chain.batch() for parsing multiple seqs at once

abnumber/__version__.py

@@ -1 +1 @@
-__version__ = '0.3.2'
+__version__ = '0.3.3'

abnumber/chain.py

@@ -1,14 +1,14 @@
 from collections import OrderedDict
 from typing import Union, List, Generator, Tuple
-from Bio import SeqIO
-from Bio.SeqRecord import SeqRecord
 import pandas as pd
 
 from abnumber.alignment import Alignment
 from abnumber.common import _anarci_align, _validate_chain_type, SUPPORTED_SCHEMES, SUPPORTED_CDR_DEFINITIONS, \
  is_integer, SCHEME_BORDERS, _get_unique_chains
 from abnumber.exceptions import ChainParseError
 import numpy as np
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
 from Bio.Seq import Seq
 
 from abnumber.position import Position
@@ -83,6 +83,8 @@ def __init__(self, sequence, scheme, cdr_definition=None, name=None, assign_germ
  else:
  if sequence is None:
  raise ChainParseError('Expected sequence, got None')
+ if isinstance(sequence, list):
+ raise ChainParseError('Expected string or Seq, got list. Please use Chain.batch() to parse multiple sequences')
  if not isinstance(sequence, str) and not isinstance(sequence, Seq):
  raise ChainParseError(f'Expected string or Seq, got {type(sequence)}: {sequence}')
  if '-' in sequence:
@@ -93,7 +95,9 @@ def __init__(self, sequence, scheme, cdr_definition=None, name=None, assign_germ
  raise ChainParseError('Do not use tail= when providing sequence=, it will be inferred automatically')
  if isinstance(sequence, Seq):
  sequence = str(sequence)
- results = _anarci_align(sequence, scheme=scheme, allowed_species=allowed_species, assign_germline=assign_germline)
+ results = _anarci_align([sequence], scheme=scheme, allowed_species=allowed_species, assign_germline=assign_germline)[0]
+ if not results:
+ raise ChainParseError(f'Variable chain sequence not recognized: "{sequence}"')
  if len(results) > 1:
  raise ChainParseError(f'Found {len(results)} antibody domains in sequence: "{sequence}"')
  aa_dict, chain_type, tail, species, v_gene, j_gene = results[0]
@@ -157,10 +161,10 @@ def _init_from_dict(self, aa_dict, allowed_species):
  else:
  seq = ''.join(aa_dict[pos] for pos in sorted_positions)
  renumbered_aa_dict = _anarci_align(
- seq,
+ [seq],
  scheme=self.cdr_definition if self.cdr_definition != 'north' else 'chothia',
  allowed_species=allowed_species
- )[0][0]
+ )[0][0][0]
  cdr_definition_positions = [pos.number for pos in sorted(renumbered_aa_dict.keys())]
  combined_aa_dict = {}
  for orig_pos, cdr_definition_position in zip(sorted_positions, cdr_definition_positions):
@@ -178,6 +182,45 @@ def _init_from_dict(self, aa_dict, allowed_species):
  region_idx += 1
  regions_list[region_idx][pos] = aa
 
+ @classmethod
+ def batch(cls, seq_dict: dict, scheme: str, cdr_definition=None, assign_germline=False, allowed_species=None):
+ """Create multiple Chain objects from dict of sequences
+
+ :param seq_dict: Dictionary of sequence strings, keys are sequence identifiers
+ :param scheme: Numbering scheme to align the sequences
+ :param cdr_definition: Numbering scheme to be used for definition of CDR regions. Same as ``scheme`` by default.
+ :param assign_germline: Assign germline name using ANARCI based on best sequence identity
+ :param allowed_species: Allowed species for germline assignment. Use ``None`` to allow all species, or one or more of: ``'human', 'mouse','rat','rabbit','rhesus','pig','alpaca'``
+ :return: tuple with (dict of Chain objects, dict of error strings)
+ """
+ assert isinstance(seq_dict, dict), f'Expected dictionary of sequences, got: {type(seq_dict).__name__}'
+ names = list(seq_dict.keys())
+ seq_list = list(seq_dict.values())
+ all_results = _anarci_align(seq_list, scheme=scheme, allowed_species=allowed_species, assign_germline=assign_germline)
+ names = names or ([None] * len(seq_list))
+ chains = {}
+ errors = {}
+ for sequence, results, name in zip(seq_list, all_results, names):
+ if not results:
+ errors[name] = f'Variable chain sequence not recognized: "{sequence}"'
+ elif len(results) > 1:
+ errors[name] = f'Found {len(results)} antibody domains: "{sequence}"'
+ else:
+ aa_dict, chain_type, tail, species, v_gene, j_gene = results[0]
+ chains[name] = Chain(
+ sequence=None,
+ aa_dict=aa_dict,
+ name=name,
+ scheme=scheme,
+ chain_type=chain_type,
+ cdr_definition=cdr_definition,
+ tail=tail,
+ species=species,
+ v_gene=v_gene,
+ j_gene=j_gene
+ )
+ return chains, errors
+
  def __repr__(self):
  return self.format()
 

abnumber/common.py

@@ -20,31 +20,34 @@ def _validate_chain_type(chain_type):
  f'Invalid chain type "{chain_type}", it should be "H" (heavy), "L" (lambda light chian) or "K" (kappa light chain)'
 
 
-def _anarci_align(sequence, scheme, allowed_species, assign_germline=False) -> List[Tuple]:
+def _anarci_align(sequences, scheme, allowed_species, assign_germline=False) -> List[List[Tuple]]:
  from abnumber.position import Position
- sequence = re.sub(WHITESPACE, '', sequence)
+ assert isinstance(sequences, list), f'Expected list of sequences, got: {type(sequences)}'
  all_numbered, all_ali, all_hits = anarci(
- [('id', sequence)],
+ [(f'id{i}', re.sub(WHITESPACE, '', sequence)) for i, sequence in enumerate(sequences)],
  scheme=scheme,
  allowed_species=allowed_species,
  assign_germline=assign_germline
  )
- seq_numbered = all_numbered[0]
- seq_ali = all_ali[0]
- if seq_numbered is None:
- raise ChainParseError(f'Variable chain sequence not recognized: "{sequence}"')
- assert len(seq_numbered) == len(seq_ali), 'Unexpected ANARCI output'
- results = []
- for (positions, start, end), ali in zip(seq_numbered, seq_ali):
- chain_type = ali['chain_type']
- species = ali['species']
- v_gene = ali['germlines']['v_gene'][0][1] if assign_germline else None
- j_gene = ali['germlines']['j_gene'][0][1] if assign_germline else None
- aa_dict = {Position(chain_type=chain_type, number=num, letter=letter, scheme=scheme): aa
- for (num, letter), aa in positions if aa != '-'}
- tail = sequence[end+1:]
- results.append((aa_dict, chain_type, tail, species, v_gene, j_gene))
- return results
+ all_results = []
+ for sequence, seq_numbered, seq_ali in zip(sequences, all_numbered, all_ali):
+ if seq_numbered is None:
+ # Variable chain sequence not recognized
+ all_results.append([])
+ continue
+ assert len(seq_numbered) == len(seq_ali), 'Unexpected ANARCI output'
+ results = []
+ for (positions, start, end), ali in zip(seq_numbered, seq_ali):
+ chain_type = ali['chain_type']
+ species = ali['species']
+ v_gene = ali['germlines']['v_gene'][0][1] if assign_germline else None
+ j_gene = ali['germlines']['j_gene'][0][1] if assign_germline else None
+ aa_dict = {Position(chain_type=chain_type, number=num, letter=letter, scheme=scheme): aa
+ for (num, letter), aa in positions if aa != '-'}
+ tail = sequence[end+1:]
+ results.append((aa_dict, chain_type, tail, species, v_gene, j_gene))
+ all_results.append(results)
+ return all_results
 
 
 def _get_unique_chains(chains):

test/test_chain.py

@@ -121,6 +121,11 @@ def test_invalid_chain_raises_error(scheme):
  Chain('AAA', scheme=scheme)
 
 
+def test_multiple_chains_raises_error():
+ with pytest.raises(ChainParseError):
+ Chain('QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSSQVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS', scheme='imgt')
+
+
 def test_aho_without_cdr_definition_raises_error():
  with pytest.raises(ValueError):
  Chain('QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS', scheme='aho')
@@ -247,3 +252,19 @@ def test_nearest_j_region():
 
  assert nearest_j[0].name == 'IGHJ6*01'
 
+
+def test_batch():
+ chains, errors = Chain.batch({
+ 'A': 'QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTVTVSS',
+ 'B': 'EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS',
+ 'C': 'FOO',
+ 'D': 'EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSSEVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS'
+ }, scheme='imgt')
+ assert len(chains) == 2
+ assert chains['A'].raw[0] == 'Q'
+ assert chains['B'].raw[0] == 'E'
+ assert 'C' not in chains
+ assert errors['C'] == 'Variable chain sequence not recognized: "FOO"'
+ assert 'D' not in chains
+ assert errors['D'] == 'Found 2 antibody domains: "EVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSSEVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYSEDDERGHYCLDYWGQGTTLTVSS"'
+