changeo.Receptor¶

Receptor data structure

class changeo.Receptor.AIRRSchema¶

Bases: object

AIRR format to Receptor mappings

custom_fields = ['c_call', 'germline_alignment_d_mask', 'v_score', 'v_identity', 'v_support', 'v_cigar', 'd_score', 'd_identity', 'd_support', 'd_cigar', 'j_score', 'j_identity', 'j_support', 'j_cigar', 'vdj_score', 'cdr1', 'cdr2', 'cdr3', 'fwr1', 'fwr2', 'fwr3', 'fwr4', 'junction_start', 'junction_end', 'cdr1_start', 'cdr1_end', 'cdr2_start', 'cdr2_end', 'cdr3_start', 'cdr3_end', 'fwr1_start', 'fwr1_end', 'fwr2_start', 'fwr2_end', 'fwr3_start', 'fwr3_end', 'fwr4_start', 'fwr4_end', 'n1_length', 'n2_length', 'p3v_length', 'p5d_length', 'p3d_length', 'p5j_length', 'd_frame', 'cdr3_igblast', 'cdr3_igblast_aa', 'duplicate_count', 'consensus_count', 'umi_count', 'clone_id', 'cell_id']¶

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', 'c_call', 'germline_alignment_d_mask', 'v_score', 'v_identity', 'v_support', 'v_cigar', 'd_score', 'd_identity', 'd_support', 'd_cigar', 'j_score', 'j_identity', 'j_support', 'j_cigar', 'vdj_score', 'cdr1', 'cdr2', 'cdr3', 'fwr1', 'fwr2', 'fwr3', 'fwr4', 'junction_start', 'junction_end', 'cdr1_start', 'cdr1_end', 'cdr2_start', 'cdr2_end', 'cdr3_start', 'cdr3_end', 'fwr1_start', 'fwr1_end', 'fwr2_start', 'fwr2_end', 'fwr3_start', 'fwr3_end', 'fwr4_start', 'fwr4_end', 'n1_length', 'n2_length', 'p3v_length', 'p5d_length', 'p3d_length', 'p5j_length', 'd_frame', 'cdr3_igblast', 'cdr3_igblast_aa', 'duplicate_count', 'consensus_count', 'umi_count', 'clone_id', 'cell_id']¶

static fromReceptor(field)¶

Returns an AIRR column name from a Receptor attribute name

Parameters:	field – Receptor attribute name.
Returns:	AIRR column name.
Return type:	str

out_type = 'tsv'¶

standard_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']¶

static toReceptor(field)¶

Returns a Receptor attribute name from an AIRR column name

Parameters:	field – AIRR column name.
Returns:	Receptor attribute name.
Return type:	str

class changeo.Receptor.ChangeoSchema¶

Bases: object

Change-O to Receptor mappings

custom_fields = ['JUNCTION_START', 'V_SCORE', 'V_IDENTITY', 'V_EVALUE', 'V_BTOP', 'V_CIGAR', 'D_SCORE', 'D_IDENTITY', 'D_EVALUE', 'D_BTOP', 'D_CIGAR', 'J_SCORE', 'J_IDENTITY', 'J_EVALUE', 'J_BTOP', 'J_CIGAR', 'VDJ_SCORE', 'FWR1_IMGT', 'FWR2_IMGT', 'FWR3_IMGT', 'FWR4_IMGT', 'CDR1_IMGT', 'CDR2_IMGT', 'CDR3_IMGT', 'N1_LENGTH', 'N2_LENGTH', 'P3V_LENGTH', 'P5D_LENGTH', 'P3D_LENGTH', 'P5J_LENGTH', 'D_FRAME', 'C_CALL', 'CDR3_IGBLAST', 'CDR3_IGBLAST_AA', 'CONSCOUNT', 'DUPCOUNT', 'UMICOUNT', 'CLONE', 'CELL']¶

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', 'JUNCTION_START', 'V_SCORE', 'V_IDENTITY', 'V_EVALUE', 'V_BTOP', 'V_CIGAR', 'D_SCORE', 'D_IDENTITY', 'D_EVALUE', 'D_BTOP', 'D_CIGAR', 'J_SCORE', 'J_IDENTITY', 'J_EVALUE', 'J_BTOP', 'J_CIGAR', 'VDJ_SCORE', 'FWR1_IMGT', 'FWR2_IMGT', 'FWR3_IMGT', 'FWR4_IMGT', 'CDR1_IMGT', 'CDR2_IMGT', 'CDR3_IMGT', 'N1_LENGTH', 'N2_LENGTH', 'P3V_LENGTH', 'P5D_LENGTH', 'P3D_LENGTH', 'P5J_LENGTH', 'D_FRAME', 'C_CALL', 'CDR3_IGBLAST', 'CDR3_IGBLAST_AA', 'CONSCOUNT', 'DUPCOUNT', 'UMICOUNT', 'CLONE', 'CELL']¶

static fromReceptor(field)¶

Returns a Change-O column name from a Receptor attribute name

Parameters:	field – Receptor attribute name.
Returns:	Change-O column name.
Return type:	str

out_type = 'tab'¶

standard_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']¶

static toReceptor(field)¶

Returns a Receptor attribute name from a Change-O column name

Parameters:	field – Change-O column name.
Returns:	Receptor attribute name.
Return type:	str

class changeo.Receptor.Receptor(data)¶

Bases: object

A class defining a V(D)J sequence and its annotations

d_germ_end¶: Position of the last nucleotide in the D germline sequence alignment

d_seq_end¶: Position of the last D nucleotide in the input sequence

getAIRR(field, seq=False)¶

Get an attribute from an AIRR field name

Parameters:	field – AIRR column name as a string seq – if True return the attribute as a Seq object
Returns:	Value in the AIRR field. Returns None if the field cannot be found.

getAlleleCalls(calls, action='first')¶

Get multiple allele calls

Parameters:	calls – iterable of calls to get; one or more of (‘v’,’d’,’j’) actions – One of (‘first’,’set’)
Returns:	List of requested calls in order
Return type:	list

getAlleleNumbers(calls, action='first')¶

Get multiple allele numeric identifiers

Parameters:	calls – iterable of calls to get; one or more of (‘v’,’d’,’j’) actions – One of (‘first’,’set’)
Returns:	List of requested calls in order
Return type:	list

getChangeo(field, seq=False)¶

Get an attribute from a Change-O field name

Parameters:	field – Change-O column name as a string seq – if True return the attribute as a Seq object
Returns:	Value in the Change-O field. Returns None if the field cannot be found.

getDAllele(action='first', field=None)¶

D segment allele getter

Parameters:	actions – One of ‘first’, ‘set’ or ‘list’ field – attribute or annotation name containing the D call. Use d_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele calls for ‘set’ or ‘list’ actions.
Return type:	str

getDAlleleNumber(action='first', field=None)¶

D segment allele number getter

Parameters:	actions – One of ‘first’, ‘set’ or list’ field – attribute or annotation name containing the D call. Use d_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele numbers for ‘set’ or ‘list’ actions.
Return type:	str

getDFamily(action='first', field=None)¶

D segment family getter

Parameters:	actions – One of ‘first’, ‘set’ or list’ field – attribute or annotation name containing the D call. Use d_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele calls for ‘set’ or ‘list’ actions.
Return type:	str

getDGene(action='first', field=None)¶

D segment gene getter

Parameters:	actions – One of ‘first’, ‘set’ or list’ field – attribute or annotation name containing the D call. Use d_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele calls for ‘set’ or ‘list’ actions.
Return type:	str

getFamilyCalls(calls, action='first')¶

Get multiple family calls

Parameters:	calls – iterable of calls to get; one or more of (‘v’,’d’,’j’) actions – One of (‘first’,’set’)
Returns:	List of requested calls in order
Return type:	list

getField(field)¶

Get an attribute or annotation value

Parameters:	field – attribute name as a string
Returns:	Value in the attribute. Returns None if the attribute cannot be found.

getGeneCalls(calls, action='first')¶

Get multiple gene calls

Parameters:	calls – iterable of calls to get; one or more of (‘v’,’d’,’j’) actions – One of (‘first’,’set’)
Returns:	List of requested calls in order
Return type:	list

getJAllele(action='first', field=None)¶

J segment allele getter

Parameters:	actions – One of ‘first’, ‘set’ or ‘list’ field – attribute or annotation name containing the J call. Use j_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele calls for ‘set’ or ‘list’ actions.
Return type:	str

getJAlleleNumber(action='first', field=None)¶

J segment allele number getter

Parameters:	actions – One of ‘first’, ‘set’ or list’ field – attribute or annotation name containing the J call. Use j_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele numbers for ‘set’ or ‘list’ actions.
Return type:	str

getJFamily(action='first', field=None)¶

J segment family getter

Parameters:	actions – One of ‘first’, ‘set’ or list’ field – attribute or annotation name containing the J call. Use j_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele calls for ‘set’ or ‘list’ actions.
Return type:	str

getJGene(action='first', field=None)¶

J segment gene getter

Parameters:	actions – One of ‘first’, ‘set’ or list’ field – attribute or annotation name containing the J call. Use j_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele calls for ‘set’ or ‘list’ actions.
Return type:	str

getSeq(field)¶

Get an attribute value converted to a Seq object

Parameters:	field – variable name as a string
Returns:	Value in the field as a Seq object
Return type:	Bio.Seq.Seq

getVAllele(action='first', field=None)¶

V segment allele getter

Parameters:	actions – One of ‘first’, ‘set’ or list’ field – attribute or annotation name containing the V call. Use v_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele calls for ‘set’ or ‘list’ actions.
Return type:	str

getVAlleleNumber(action='first', field=None)¶

V segment allele number getter

Parameters:	actions – One of ‘first’, ‘set’ or list’ field – attribute or annotation name containing the V call. Use v_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele numbers for ‘set’ or ‘list’ actions.
Return type:	str

getVFamily(action='first', field=None)¶

V segment family getter

Parameters:	actions – One of ‘first’, ‘set’ or list’ field – attribute or annotation name containing the V call. Use v_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele calls for ‘set’ or ‘list’ actions.
Return type:	str

getVGene(action='first', field=None)¶

V segment gene getter

Parameters:	actions – One of ‘first’, ‘set’ or list’ field – attribute or annotation name containing the V call. Use v_call attribute if None.
Returns:	String of the allele when action is ‘first’; tuple : Tuple of allele calls for ‘set’ or ‘list’ actions.
Return type:	str

j_germ_end¶: Position of the last nucleotide in the J germline sequence alignment

j_seq_end¶: Position of the last J nucleotide in the input sequence

junction_end¶: Position of the last junction nucleotide in the input sequence

setDict(data, parse=False)¶

Adds or updates multiple attributes and annotations

Parameters:	data – a dictionary of annotations to add or update. parse – if True pass values through string parsing functions for known fields.
Returns:	updates attribute values and the annotations attribute.
Return type:	None

setField(field, value, parse=False)¶

Set an attribute or annotation value

Parameters:	field – attribute name as a string value – value to assign parse – if True pass values through string parsing functions for known fields.
Returns:	None. Updates attribute or annotation.

toDict()¶

Convert the namespace to a dictionary

Returns:	member fields with values converted to appropriate strings
Return type:	dict

v_germ_end_imgt¶: Position of the last nucleotide in the IMGT-gapped V germline sequence alignment

v_germ_end_vdj¶: Position of the last nucleotide in the ungapped V germline sequence alignment

v_seq_end¶: Position of the last V nucleotide in the input sequence

class changeo.Receptor.ReceptorData¶

Bases: object

A class containing type conversion methods for Receptor data attributes

sequence_id¶

unique sequence identifier.

Type:	str

rev_comp¶

whether the alignment is relative to the reverse compliment of the input sequence.

Type:	bool

functional¶

whether sample V(D)J sequence is predicted to be functional.

Type:	bool

in_frame¶

whether junction region is in-frame.

Type:	bool

stop¶

whether a stop codon is present in the V(D)J sequence.

Type:	bool

mutated_invariant¶

whether the conserved amino acids are mutated in the V(D)J sequence.

Type:	bool

indels¶

whether the V(D)J nucleotide sequence contains insertions and/or deletions.

Type:	bool

sequence_input¶

input nucleotide sequence.

Type:	Bio.Seq.Seq

sequence_vdj¶

Aligned V(D)J nucleotide sequence without IMGT-gaps.

Type:	Bio.Seq.Seq

sequence_imgt¶

IMGT-gapped V(D)J nucleotide sequence.

Type:	Bio.Seq.Seq

junction¶

ungapped junction region nucletide sequence.

Type:	Bio.Seq.Seq

junction_aa¶

ungapped junction region amino acid sequence.

Type:	Bio.Seq.Seq

junction_start¶

start positions of the junction in the input nucleotide sequence.

Type:	int

junction_length¶

length of the junction in nucleotides.

Type:	int

germline_vdj¶

full ungapped germline V(D)J nucleotide sequence.

Type:	Bio.Seq.Seq

germline_vdj_d_mask¶

ungapped germline V(D)J nucleotides sequence with Ns masking the NP1-D-NP2 regions.

Type:	Bio.Seq.Seq

germline_imgt¶

full IMGT-gapped germline V(D)J nucleotide sequence.

Type:	Bio.Seq.Seq

germline_imgt_d_mask¶

IMGT-gapped germline V(D)J nucleotide sequence with ns masking the NP1-D-NP2 regions.

Type:	Bio.Seq.Seq

v_call¶

V allele assignment(s).

Type:	str

d_call¶

D allele assignment(s).

Type:	str

j_call¶

J allele assignment(s).

Type:	str

c_call¶

C region assignment.

Type:	str

v_seq_start¶

position of the first V nucleotide in the input sequence (1-based).

Type:	int

v_seq_length¶

number of V nucleotides in the input sequence.

Type:	int

v_germ_start_imgt¶

position of the first V nucleotide in IMGT-gapped V germline sequence alignment (1-based).

Type:	int

v_germ_length_imgt¶

length of the IMGT numbered germline V alignment.

Type:	int

v_germ_start_vdj¶

position of the first nucleotide in ungapped V germline sequence alignment (1-based).

Type:	int

v_germ_length_vdj¶

length of the ungapped germline V alignment.

Type:	int

np1_start¶

position of the first untemplated nucleotide between the V and D segments in the input sequence (1-based).

Type:	int

np1_length¶

number of untemplated nucleotides between the V and D segments.

Type:	int

d_seq_start¶

position of the first D nucleotide in the input sequence (1-based).

Type:	int

d_seq_length¶

number of D nucleotides in the input sequence.

Type:	int

d_germ_start¶

position of the first nucleotide in D germline sequence alignment (1-based).

Type:	int

d_germ_length¶

length of the germline D alignment.

Type:	int

np2_start¶

position of the first untemplated nucleotide between the D and J segments in the input sequence (1-based).

Type:	int

np2_length¶

number of untemplated nucleotides between the D and J segments.

Type:	int

j_seq_start¶

position of the first J nucleotide in the input sequence (1-based).

Type:	int

j_seq_length¶

number of J nucleotides in the input sequence.

Type:	int

j_germ_start¶

position of the first nucleotide in J germline sequence alignment (1-based).

Type:	int

j_germ_length¶

length of the germline J alignment.

Type:	int

v_score¶

alignment score for the V.

Type:	float

v_identity¶

alignment identity for the V.

Type:	float

v_evalue¶

E-value for the alignment of the V.

Type:	float

v_btop¶

BTOP for the alignment of the V.

Type:	str

v_cigar¶

CIGAR for the alignment of the V.

Type:	str

d_score¶

alignment score for the D.

Type:	float

d_identity¶

alignment identity for the D.

Type:	float

d_evalue¶

E-value for the alignment of the D.

Type:	float

d_btop¶

BTOP for the alignment of the D.

Type:	str

d_cigar¶

CIGAR for the alignment of the D.

Type:	str

j_score¶

alignment score for the J.

Type:	float

j_identity¶

alignment identity for the J.

Type:	float

j_evalue¶

E-value for the alignment of the J.

Type:	float

j_btop¶

BTOP for the alignment of the J.

Type:	str

j_cigar¶

CIGAR for the alignment of the J.

Type:	str

vdj_score¶

alignment score for the V(D)J.

Type:	float

fwr1_imgt¶

IMGT-gapped FWR1 nucleotide sequence.

Type:	Bio.Seq.Seq

fwr2_imgt¶

IMGT-gapped FWR2 nucleotide sequence.

Type:	Bio.Seq.Seq

fwr3_imgt¶

IMGT-gapped FWR3 nucleotide sequence.

Type:	Bio.Seq.Seq

fwr4_imgt¶

IMGT-gapped FWR4 nucleotide sequence.

Type:	Bio.Seq.Seq

cdr1_imgt¶

IMGT-gapped CDR1 nucleotide sequence.

Type:	Bio.Seq.Seq

cdr2_imgt¶

IMGT-gapped CDR2 nucleotide sequence.

Type:	Bio.Seq.Seq

cdr3_imgt¶

IMGT-gapped CDR3 nucleotide sequence.

Type:	Bio.Seq.Seq

cdr3_igblast¶

CDR3 nucleotide sequence assigned by IgBLAST.

Type:	Bio.Seq.Seq

cdr3_igblast_aa¶

CDR3 amino acid sequence assigned by IgBLAST.

Type:	Bio.Seq.Seq

n1_length¶

M nucleotides 5’ of the D segment.

Type:	int

n2_length¶

nucleotides 3’ of the D segment.

Type:	int

p3v_length¶

palindromic nucleotides 3’ of the V segment.

Type:	int

p5d_length¶

palindromic nucleotides 5’ of the D segment.

Type:	int

p3d_length¶

palindromic nucleotides 3’ of the D segment.

Type:	int

p5j_length¶

palindromic nucleotides 5’ of the J segment.

Type:	int

d_frame¶

D segment reading frame.

Type:	int

conscount¶

number of reads contributing to the UMI consensus sequence.

Type:	int

dupcount¶

copy number of the sequence.

Type:	int

umicount¶

number of UMIs representing the sequence.

Type:	int

clone¶

clonal cluster identifier.

Type:	str

cell¶

origin cell identifier.

Type:	str

annotations¶

dictionary containing all unknown fields.

Type:	dict

static aminoacid(v, deparse=False)¶

static double(v, deparse=False)¶

end_fields = {'cdr1_end': ('cdr1_start', 'cdr1_length'), 'cdr2_end': ('cdr2_start', 'cdr2_length'), 'cdr3_end': ('cdr3_start', 'cdr3_length'), 'd_alignment_end': ('d_alignment_start', 'd_alignment_length'), 'd_germ_end': ('d_germ_start', 'd_germ_length'), 'd_seq_end': ('d_seq_start', 'd_seq_length'), 'fwr1_end': ('fwr1_start', 'fwr1_length'), 'fwr2_end': ('fwr2_start', 'fwr2_length'), 'fwr3_end': ('fwr3_start', 'fwr3_length'), 'fwr4_end': ('fwr4_start', 'fwr4_length'), 'j_alignment_end': ('j_alignment_start', 'j_alignment_length'), 'j_germ_end': ('j_germ_start', 'j_germ_length'), 'j_seq_end': ('j_seq_start', 'j_seq_length'), 'junction_end': ('junction_start', 'junction_length'), 'v_alignment_end': ('v_alignment_start', 'v_alignment_length'), 'v_germ_end_imgt': ('v_germ_start_imgt', 'v_germ_length_imgt'), 'v_germ_end_vdj': ('v_germ_start_vdj', 'v_germ_length_vdj'), 'v_seq_end': ('v_seq_start', 'v_seq_length')}¶

static identity(v, deparse=False)¶

static integer(v, deparse=False)¶

length_fields = {'cdr1_length': ('cdr1_start', 'cdr1_end'), 'cdr2_length': ('cdr2_start', 'cdr2_end'), 'cdr3_length': ('cdr3_start', 'cdr3_end'), 'd_alignment_length': ('d_alignment_start', 'd_alignment_end'), 'd_germ_length': ('d_germ_start', 'd_germ_end'), 'd_seq_length': ('d_seq_start', 'd_seq_end'), 'fwr1_length': ('fwr1_start', 'fwr1_end'), 'fwr2_length': ('fwr2_start', 'fwr2_end'), 'fwr3_length': ('fwr3_start', 'fwr3_end'), 'fwr4_length': ('fwr4_start', 'fwr4_end'), 'j_alignment_length': ('j_alignment_start', 'j_alignment_end'), 'j_germ_length': ('j_germ_start', 'j_germ_end'), 'j_seq_length': ('j_seq_start', 'j_seq_end'), 'junction_length': ('junction_start', 'junction_end'), 'v_alignment_length': ('v_alignment_start', 'v_alignment_end'), 'v_germ_length_imgt': ('v_germ_start_imgt', 'v_germ_end_imgt'), 'v_germ_length_vdj': ('v_germ_start_vdj', 'v_germ_end_vdj'), 'v_seq_length': ('v_seq_start', 'v_seq_end')}¶

static logical(v, deparse=False)¶

static nucleotide(v, deparse=False)¶

parsers = {'c_call': 'identity', 'cdr1_imgt': 'nucleotide', 'cdr2_imgt': 'nucleotide', 'cdr3_igblast': 'nucleotide', 'cdr3_igblast_aa': 'aminoacid', 'cdr3_imgt': 'nucleotide', 'cell': 'identity', 'clone': 'identity', 'conscount': 'integer', 'd_btop': 'identity', 'd_call': 'identity', 'd_cigar': 'identity', 'd_evalue': 'double', 'd_frame': 'integer', 'd_germ_length': 'integer', 'd_germ_start': 'integer', 'd_identity': 'double', 'd_score': 'double', 'd_seq_length': 'integer', 'd_seq_start': 'integer', 'dupcount': 'integer', 'functional': 'logical', 'fwr1_imgt': 'nucleotide', 'fwr2_imgt': 'nucleotide', 'fwr3_imgt': 'nucleotide', 'fwr4_imgt': 'nucleotide', 'germline_imgt': 'nucleotide', 'germline_imgt_d_mask': 'nucleotide', 'germline_vdj': 'nucleotide', 'germline_vdj_d_mask': 'nucleotide', 'in_frame': 'logical', 'indels': 'logical', 'j_btop': 'identity', 'j_call': 'identity', 'j_cigar': 'identity', 'j_evalue': 'double', 'j_germ_length': 'integer', 'j_germ_start': 'integer', 'j_identity': 'double', 'j_score': 'double', 'j_seq_length': 'integer', 'j_seq_start': 'integer', 'junction': 'nucleotide', 'junction_aa': 'aminoacid', 'junction_length': 'integer', 'junction_start': 'integer', 'locus': 'identity', 'mutated_invariant': 'logical', 'n1_length': 'integer', 'n2_length': 'integer', 'np1_length': 'integer', 'np1_start': 'integer', 'np2_length': 'integer', 'np2_start': 'integer', 'p3d_length': 'integer', 'p3v_length': 'integer', 'p5d_length': 'integer', 'p5j_length': 'integer', 'rev_comp': 'logical', 'sequence_id': 'identity', 'sequence_imgt': 'nucleotide', 'sequence_input': 'nucleotide', 'sequence_vdj': 'nucleotide', 'stop': 'logical', 'umicount': 'integer', 'v_btop': 'identity', 'v_call': 'identity', 'v_cigar': 'identity', 'v_evalue': 'double', 'v_germ_length_imgt': 'integer', 'v_germ_length_vdj': 'integer', 'v_germ_start_imgt': 'integer', 'v_germ_start_vdj': 'integer', 'v_identity': 'double', 'v_score': 'double', 'v_seq_length': 'integer', 'v_seq_start': 'integer', 'vdj_score': 'double'}¶

start_fields = {'cdr1_start': ('cdr1_length', 'cdr1_end'), 'cdr2_start': ('cdr2_length', 'cdr2_end'), 'cdr3_start': ('cdr3_length', 'cdr3_end'), 'd_alignment_start': ('d_alignment_length', 'd_alignment_end'), 'd_germ_start': ('d_germ_length', 'd_germ_end'), 'd_seq_start': ('d_seq_length', 'd_seq_end'), 'fwr1_start': ('fwr1_length', 'fwr1_end'), 'fwr2_start': ('fwr2_length', 'fwr2_end'), 'fwr3_start': ('fwr3_length', 'fwr3_end'), 'fwr4_start': ('fwr4_length', 'fwr4_end'), 'j_alignment_start': ('j_alignment_length', 'j_alignment_end'), 'j_germ_start': ('j_germ_length', 'j_germ_end'), 'j_seq_start': ('j_seq_length', 'j_seq_end'), 'junction_start': ('junction_length', 'junction_end'), 'v_alignment_start': ('v_alignment_length', 'v_alignment_end'), 'v_germ_start_imgt': ('v_germ_length_imgt', 'v_germ_end_imgt'), 'v_germ_start_vdj': ('v_germ_length_vdj', 'v_germ_end_vdj'), 'v_seq_start': ('v_seq_length', 'v_seq_end')}¶