changeo.Alignment¶
Alignment manipulation
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class
changeo.Alignment.
RegionDefinition
(junction_length, amino_acid=False, definition='default')¶ Bases:
object
FWR and CDR region boundary definitions
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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
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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
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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
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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
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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, regions='default')¶ 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.
regions (str) – name of the IMGT FWR/CDR region definitions to use.
- 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