changeo.Gene¶
Gene annotations
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changeo.Gene.buildClonalGermline(receptors, references, seq_field='SEQUENCE_IMGT', v_field='V_CALL', d_field='D_CALL', j_field='J_CALL')¶ Determine consensus clone sequence and create germline for clone
Parameters: - receptors – list of Receptor objects
- references – dictionary of IMGT gapped germline sequences
- seq_field – field in which to look for sequence
- v_field – field in which to look for V call
- d_field – field in which to look for D call
- j_field – field in which to look for J call
Returns: - log dictionary, dictionary of {germline_type: germline_sequence},
dictionary of consensus {segment: gene call}
Return type:
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changeo.Gene.buildGermline(receptor, references, seq_field='SEQUENCE_IMGT', v_field='V_CALL', d_field='D_CALL', j_field='J_CALL')¶ Join gapped germline sequences aligned with sample sequences
Parameters: - receptor – Receptor object
- references – dictionary of IMGT gapped germline sequences
- seq_field – field in which to look for sequence
- v_field – field in which to look for V call
- d_field – field in which to look for V call
- j_field – field in which to look for V call
Returns: log dictionary, dictionary of {germline_type: germline_sequence}, dictionary of {segment: gene call}
Return type:
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changeo.Gene.getDGermline(receptor, references, d_field='D_CALL')¶ Extract D allele and germline sequence
Parameters: - receptor – Receptor object
- references – dictionary of germline sequences
- d_field – field containing the D allele assignment
Returns: D allele name, D segment germline sequence
Return type:
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changeo.Gene.getJGermline(receptor, references, j_field='J_CALL')¶ Extract J allele and germline sequence
Parameters: - receptor – Receptor object
- references – dictionary of germline sequences
- j_field – field containing the J allele assignment
Returns: J allele name, J segment germline sequence
Return type:
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changeo.Gene.getVGermline(receptor, references, v_field='V_CALL')¶ Extract V allele and germline sequence
Parameters: - receptor – Receptor object
- references – dictionary of germline sequences
- v_field – field containing the V allele assignment
Returns: V allele name, V segment germline sequence
Return type:
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changeo.Gene.parseAllele(alleles, regex, action='first')¶ Extract alleles from strings
Parameters: - alleles – string with allele calls
- regex – compiled regular expression for allele match
- action – action to perform for multiple alleles; one of (‘first’, ‘set’, ‘list’).
Returns: String of the allele when action is ‘first’; tuple : Tuple of allele calls for ‘set’ or ‘list’ actions.
Return type:
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changeo.Gene.stitchRegions(receptor, v_seq, d_seq, j_seq)¶ Assemble full length region encoding
Parameters: - receptor – Receptor object
- v_seq – V segment germline sequence as a string
- d_seq – D segment germline sequence as a string
- j_seq – J segment germline sequence as a string
Returns: string defining germline regions
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