changeo.Alignment¶
Alignment manipulation
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changeo.Alignment.
alignmentPositions
(alignment)¶ Extracts start position and length from an alignment
Parameters: alignment – tuples of (operation, length) for each alignment operation. Returns: - query (q) and reference (r) start (0-based) and length information with keys
- {q_start, q_length, r_start, r_length}.
Return type: dict
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changeo.Alignment.
decodeBTOP
(btop)¶ Parse a BTOP string into a list of tuples in CIGAR annotation.
Parameters: btop – BTOP string. Returns: tuples of (operation, length) for each operation in the BTOP string using CIGAR annotation. Return type: list
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changeo.Alignment.
decodeCIGAR
(cigar)¶ Parse a CIGAR string into a list of tuples.
Parameters: cigar – CIGAR string. Returns: tuples of (operation, length) for each operation in the CIGAR string. Return type: list
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changeo.Alignment.
encodeCIGAR
(alignment)¶ Encodes a list of tuple with alignment information into a CIGAR string.
Parameters: tuple – tuples of (type, length) for each alignment operation. Returns: CIGAR string. Return type: str
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changeo.Alignment.
gapV
(seq, v_germ_start, v_germ_length, v_call, references, asis_calls=False)¶ Construction IMGT-gapped V segment sequences.
Parameters: - seq (str) – V(D)J sequence alignment (SEQUENCE_VDJ).
- v_germ_start (int) – start position V segment alignment in the germline (V_GERM_START_VDJ, 1-based).
- v_germ_length (int) – length of the V segment alignment against the germline (V_GERM_LENGTH_VDJ, 1-based).
- v_call (str) – V segment allele assignment (V_CALL).
- references (dict) – dictionary of IMGT-gapped reference sequences.
- asis_calls (bool) – if True do not parse v_call for allele names and just split by comma.
Returns: dictionary containing IMGT-gapped query sequences and germline positions.
Return type: Raises: KeyError
– raised if the v_call is not found in the reference dictionary.
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changeo.Alignment.
getRegions
(seq, junction_length)¶ Identify FWR and CDR regions by IMGT definition.
Parameters: - seq – IMGT-gapped sequence.
- junction_length – length of the junction region in nucleotides.
Returns: dictionary of FWR and CDR sequences.
Return type:
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changeo.Alignment.
inferJunction
(seq, j_germ_start, j_germ_length, j_call, references, asis_calls=False)¶ Identify junction region by IMGT definition.
Parameters: - seq (str) – IMGT-gapped V(D)J sequence alignment (SEQUENCE_IMGT).
- j_germ_start (int) – start position J segment alignment in the germline (J_GERM_START, 1-based).
- j_germ_length (int) – length of the J segment alignment against the germline (J_GERM_LENGTH).
- j_call (str) – J segment allele assignment (J_CALL).
- references (dict) – dictionary of IMGT-gapped reference sequences.
- asis_calls (bool) – if True do not parse V_CALL for allele names and just split by comma.
Returns: dictionary containing junction sequence, translation and length.
Return type:
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changeo.Alignment.
padAlignment
(alignment, q_start, r_start)¶ Pads the start of an alignment based on query and reference positions.
Parameters: - alignment – tuples of (operation, length) for each alignment operation.
- q_start – query (input) start position (0-based)
- r_start – reference (subject) start position (0-based)
Returns: updated list of tuples of (operation, length) for the alignment.
Return type: