changeo.Parsers¶
Alignment tool parsing functions
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class
changeo.Parsers.
IHMMuneReader
(ihmmune, seq_dict, repo_dict, parse_scores=False, parse_regions=False, ig=True)¶ Bases:
object
An iterator to read and parse iHMMune-Align output files.
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__iter__
()¶ Iterator initializer.
Returns: changeo.Parsers.IHMMuneReader
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__next__
()¶ Next method.
Returns: parsed IMGT/HighV-QUEST result as an IgRecord (ig=True) or dictionary (ig=False). Return type: changeo.Receptor.IgRecord
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fields
¶ List of ordered output field names.
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ihmmune_fields
= ['SEQUENCE_ID', 'V_CALL', 'D_CALL', 'J_CALL', 'V_SEQ', 'NP1_SEQ', 'D_SEQ', 'NP2_SEQ', 'J_SEQ', 'V_MUT', 'D_MUT', 'J_MUT', 'NX_COUNT', 'J_INFRAME', 'V_SEQ_START', 'STOP_COUNT', 'D_PROB', 'HMM_SCORE', 'RC', 'COMMON_MUT', 'COMMON_NX_COUNT', 'V_SEQ_START2', 'V_SEQ_LENGTH', 'A_SCORE']¶
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class
changeo.Parsers.
IMGTReader
(summary, gapped, ntseq, junction, parse_scores=False, parse_regions=False, parse_junction=False, ig=True)¶ Bases:
object
An iterator to read and parse IMGT output files.
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__iter__
()¶ Iterator initializer.
Returns: changeo.Parsers.IgBLASTReader
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__next__
()¶ Next method.
Returns: parsed IMGT/HighV-QUEST result as an IgRecord (ig=True) or dictionary (ig=False). Return type: changeo.Receptor.IgRecord
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fields
¶ List of ordered output field names.
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parseRecord
(summary, gapped, ntseq, junction)¶ Parses a single row from each IMTG file.
Parameters: - summary – dictionary containing one row of the ‘1_Summary’ file.
- gapped – dictionary containing one row of the ‘2_IMGT-gapped-nt-sequences’ file.
- ntseq – dictionary containing one row of the ‘3_Nt-sequences’ file.
- junction – dictionary containing one row of the ‘6_Junction’ file.
Returns: database entry for the row.
Return type:
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class
changeo.Parsers.
IgBLASTReader
(igblast, seq_dict, repo_dict, parse_scores=False, parse_regions=False, parse_igblast_cdr3=False, ig=True)¶ Bases:
object
An iterator to read and parse IgBLAST output files
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__iter__
()¶ Iterator initializer.
Returns: changeo.Parsers.IgBLASTReader
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__next__
()¶ Next method.
Returns: parsed IMGT/HighV-QUEST result as an IgRecord (ig=True) or dictionary (ig=False). Return type: changeo.Receptor.IgRecord
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fields
¶ List of ordered output field names.
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parseBlock
(block)¶ Parses an IgBLAST result into separate sections
Parameters: block – an iterator from itertools.groupby containing a single IgBLAST result. Returns: - a parsed results block;
- with the keys ‘query’ (sequence identifier as a string), ‘summary’ (dictionary of the alignment summary), ‘subregion’ (dictionary of IgBLAST CDR3 sequences), and ‘hits’ (VDJ hit table as a list of dictionaries). Returns None if the block has no data that can be parsed.
Return type: dict
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changeo.Parsers.
decodeBTOP
(btop)¶ Parse a BTOP string into a list of tuples.
Parameters: btop – BTOP string. Returns: tuples of (type, length) for each operation in the BTOP string. Return type: list
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changeo.Parsers.
decodeCIGAR
(cigar)¶ Parse a CIGAR string into a list of tuples.
Parameters: cigar – CIGAR string. Returns: tuples of (type, length) for each operation in the CIGAR string. Return type: list
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changeo.Parsers.
encodeCIGAR
(alignment)¶ Encodes a list of tuple with alignment information into a CIGAR string.
Parameters: alignment – tuples of (type, length) for each alignment operation. Returns: CIGAR string. Return type: str
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changeo.Parsers.
gapV
(db, repo_dict)¶ Construction IMGT-gapped V-region sequences.
Parameters: - db – database dictionary of parsed IgBLAST.
- repo_dict – dictionary of IMGT-gapped reference sequences.
Returns: database entries containing IMGT-gapped query sequences and germline positions.
Return type:
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changeo.Parsers.
getIDforIMGT
(seq_file)¶ Create a sequence ID translation using IMGT truncation.
Parameters: seq_file – a fasta file of sequences input to IMGT. Returns: a dictionary of with the IMGT truncated ID as the key and the full sequence description as the value. Return type: dict