changeo.IO¶
File I/O and parsers
-
class
changeo.IO.
AIRRReader
(handle)¶ Bases:
changeo.IO.TSVReader
An iterator to read and parse AIRR formatted data.
-
class
changeo.IO.
AIRRWriter
(handle, fields=['sequence_id', 'sequence', 'sequence_alignment', 'germline_alignment', 'rev_comp', 'productive', 'stop_codon', 'vj_in_frame', 'locus', 'v_call', 'd_call', 'j_call', 'junction', 'junction_length', 'junction_aa', 'np1_length', 'np2_length', 'v_sequence_start', 'v_sequence_end', 'v_germline_start', 'v_germline_end', 'd_sequence_start', 'd_sequence_end', 'd_germline_start', 'd_germline_end', 'j_sequence_start', 'j_sequence_end', 'j_germline_start', 'j_germline_end'])¶ Bases:
changeo.IO.TSVWriter
Writes AIRR formatted data.
-
writeReceptor
(records)¶ Writes a row from a Receptor object
Parameters: records – a changeo.Receptor object to write or iterable of such objects. Returns: None
-
-
class
changeo.IO.
ChangeoReader
(handle)¶ Bases:
changeo.IO.TSVReader
An iterator to read and parse Change-O formatted data.
-
class
changeo.IO.
ChangeoWriter
(handle, fields=['SEQUENCE_ID', 'SEQUENCE_INPUT', 'FUNCTIONAL', 'IN_FRAME', 'STOP', 'MUTATED_INVARIANT', 'INDELS', 'LOCUS', 'V_CALL', 'D_CALL', 'J_CALL', 'SEQUENCE_VDJ', 'SEQUENCE_IMGT', 'V_SEQ_START', 'V_SEQ_LENGTH', 'V_GERM_START_VDJ', 'V_GERM_LENGTH_VDJ', 'V_GERM_START_IMGT', 'V_GERM_LENGTH_IMGT', 'NP1_LENGTH', 'D_SEQ_START', 'D_SEQ_LENGTH', 'D_GERM_START', 'D_GERM_LENGTH', 'NP2_LENGTH', 'J_SEQ_START', 'J_SEQ_LENGTH', 'J_GERM_START', 'J_GERM_LENGTH', 'JUNCTION', 'JUNCTION_LENGTH', 'GERMLINE_IMGT'], header=True)¶ Bases:
changeo.IO.TSVWriter
Writes Change-O formatted data.
-
writeReceptor
(records)¶ Writes a row from a Receptor object
Parameters: records – a changeo.Receptor.Receptor object to write or an iterable of such objects. Returns: None
-
-
class
changeo.IO.
IHMMuneReader
(ihmmune, sequences, references, receptor=True)¶ Bases:
object
An iterator to read and parse iHMMune-Align output files.
-
__iter__
()¶ Iterator initializer.
Returns: changeo.IO.IHMMuneReader
-
__next__
()¶ Next method.
Returns: parsed IMGT/HighV-QUEST result as an Receptor (receptor=True) or dictionary (receptor=False). Return type: changeo.Receptor.Receptor
-
static
customFields
(scores=False, regions=False, cell=False, schema=None)¶ Returns non-standard Receptor attributes defined by the parser
Parameters: - scores – if True include alignment scoring fields.
- regions – if True include IMGT-gapped CDR and FWR region fields.
- schema – schema class to pass field through for conversion. If None, return changeo.Receptor.Receptor attribute names.
Returns: list of field names.
Return type:
-
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_START', 'V_SEQ_LENGTH', 'A_SCORE']¶
-
-
class
changeo.IO.
IMGTReader
(summary, gapped, ntseq, junction, receptor=True)¶ Bases:
object
An iterator to read and parse IMGT output files.
-
__iter__
()¶ Iterator initializer.
Returns: changeo.IO.IMGTReader
-
__next__
()¶ Next method.
Returns: parsed IMGT/HighV-QUEST result as an Receptor (receptor=True) or dictionary (receptor=False). Return type: changeo.Receptor.Receptor
-
static
customFields
(scores=False, regions=False, junction=False, schema=None)¶ Returns non-standard fields defined by the parser
Parameters: - scores – if True include alignment scoring fields.
- regions – if True include IMGT-gapped CDR and FWR region fields.
- junction – if True include detailed junction annotation fields.
- schema – schema class to pass field through for conversion. If None, return changeo.Receptor.Receptor attribute names.
Returns: list of field names.
Return type:
-
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:
-
-
class
changeo.IO.
IgBLASTReader
(igblast, sequences, references, asis_calls=False, receptor=True)¶ Bases:
object
An iterator to read and parse IgBLAST output files
-
__iter__
()¶ Iterator initializer.
Returns: changeo.IO.IgBLASTReader
-
__next__
()¶ Next method.
Returns: parsed IMGT/HighV-QUEST result as an Receptor (receptor=True) or dictionary (receptor=False). Return type: changeo.Receptor.Receptor
-
static
customFields
(scores=False, regions=False, cdr3=False, schema=None)¶ Returns non-standard fields defined by the parser
Parameters: - scores – if True include alignment scoring fields.
- regions – if True include IMGT-gapped CDR and FWR region fields.
- cdr3 – if True include IgBLAST CDR3 assignment fields.
- schema – schema class to pass field through for conversion. If None, return changeo.Receptor.Receptor attribute names.
Returns: list of field names.
Return type:
-
parseBlock
(block)¶ Parses an IgBLAST result into separate sections
Parameters: block (iter) – 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
-
-
class
changeo.IO.
TSVReader
(handle)¶ Bases:
object
Simple csv.DictReader wrapper to read format agnostic TSV files.
-
reader
¶ reader object.
Type: iter
-
__iter__
()¶ Iterator initializer
Returns: changeo.IO.TSVReader
-
__next__
()¶ Next method
Returns: row as a dictionary of field:value pairs. Return type: dist
-
-
class
changeo.IO.
TSVWriter
(handle, fields, header=True)¶ Bases:
object
Simple csv.DictWriter wrapper to write format agnostic TSV files.
-
writeDict
(records)¶ Writes a row from a dictionary
Parameters: records – dictionary of row data or an iterable of such objects. Returns: None
-
writeHeader
()¶ Writes the header
Returns: None
-
-
changeo.IO.
checkFields
(attributes, header, schema=<class 'changeo.Receptor.ChangeoSchema'>)¶ Checks that a file header contains a required set of Receptor attributes
Parameters: Returns: True if all attributes mapping fields are found.
Return type: Raises:
-
changeo.IO.
countDbFile
(file)¶ Counts the records in database files
Parameters: file – tab-delimited database file. Returns: count of records in the database file. Return type: int
-
changeo.IO.
extractIMGT
(imgt_output)¶ Extract necessary files from IMGT/HighV-QUEST results.
Parameters: imgt_output – zipped file or unzipped folder output by IMGT/HighV-QUEST. Returns: (temporary directory handle, dictionary with names of extracted IMGT files). Return type: tuple
-
changeo.IO.
getDbFields
(file, add=None, exclude=None, reader=<class 'changeo.IO.TSVReader'>)¶ Get field names from a db file
Parameters: - file – db file to pull base fields from.
- add – fields to append to the field set.
- exclude – fields to exclude from the field set.
- reader – reader class.
Returns: list of field names
Return type:
-
changeo.IO.
getFormatOperators
(format)¶ Simple wrapper for fetching the set of operator classes for a data format
Parameters: format (str) – name of the data format. Returns: a tuple with the reader class, writer class, and schema definition class. Return type: tuple
-
changeo.IO.
getOutputHandle
(file, out_label=None, out_dir=None, out_name=None, out_type=None)¶ Opens an output file handle
Parameters: - file – filename to base output file name on.
- out_label – text to be inserted before the file extension; if None do not add a label.
- out_type – the file extension of the output file; if None use input file extension.
- out_dir – the output directory; if None use directory of input file
- out_name – the short filename to use for the output file; if None use input file short name.
Returns: File handle
Return type: file
-
changeo.IO.
getOutputName
(file, out_label=None, out_dir=None, out_name=None, out_type=None)¶ Creates and output filename from an existing filename
Parameters: - file – filename to base output file name on.
- out_label – text to be inserted before the file extension; if None do not add a label.
- out_type – the file extension of the output file; if None use input file extension.
- out_dir – the output directory; if None use directory of input file
- out_name – the short filename to use for the output file; if None use input file short name.
Returns: file name.
Return type:
-
changeo.IO.
readGermlines
(references, asis=False)¶ Parses germline repositories
Parameters: Returns: Dictionary of germlines in the form {allele: sequence}.
Return type: