changeo.Receptor

Receptor data structure

class changeo.Receptor.AIRRSchema

Bases: object

AIRR format to Receptor mappings

fields = ['sequence_id', 'sequence', 'sequence_alignment', 'germline_alignment', 'sequence_aa', 'sequence_aa_alignment', 'germline_aa_alignment', 'rev_comp', 'productive', 'stop_codon', 'vj_in_frame', 'v_frameshift', 'locus', 'v_call', 'd_call', 'j_call', 'c_call', 'junction', 'junction_start', 'junction_end', 'junction_length', 'junction_aa', 'junction_aa_length', 'np1_length', 'np2_length', 'np1_aa_length', 'np2_aa_length', 'v_sequence_start', 'v_sequence_end', 'v_sequence_length', 'v_germline_start', 'v_germline_end', 'v_germline_length', 'v_sequence_aa_start', 'v_sequence_aa_end', 'v_sequence_aa_length', 'v_germline_aa_start', 'v_germline_aa_end', 'v_germline_aa_length', 'd_sequence_start', 'd_sequence_end', 'd_sequence_length', 'd_germline_start', 'd_germline_end', 'd_germline_length', 'd_sequence_aa_start', 'd_sequence_aa_end', 'd_sequence_aa_length', 'd_germline_aa_start', 'd_germline_aa_end', 'd_germline_aa_length', 'j_sequence_start', 'j_sequence_end', 'j_sequence_length', 'j_germline_start', 'j_germline_end', 'j_germline_length', 'j_sequence_aa_start', 'j_sequence_aa_end', 'j_sequence_aa_length', 'j_germline_aa_start', 'j_germline_aa_end', 'j_germline_aa_length', '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', 'cdr1_aa', 'cdr2_aa', 'cdr3_aa', 'fwr1_aa', 'fwr2_aa', 'fwr3_aa', 'fwr4_aa', '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'
required = ['sequence_id', 'sequence', 'sequence_alignment', 'germline_alignment', 'rev_comp', 'productive', 'stop_codon', 'vj_in_frame', 'locus', 'v_call', 'd_call', 'j_call', 'c_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.AIRRSchemaAA

Bases: changeo.Receptor.AIRRSchema

AIRR format to Receptor amino acid mappings

required = ['sequence_id', 'sequence', 'sequence_alignment', 'germline_alignment', 'sequence_aa', 'sequence_aa_alignment', 'germline_aa_alignment', 'rev_comp', 'productive', 'stop_codon', 'locus', 'v_call', 'd_call', 'j_call', 'c_call', 'junction', 'junction_length', 'junction_aa', 'v_sequence_aa_start', 'v_sequence_aa_end', 'v_germline_aa_start', 'v_germline_aa_end']
class changeo.Receptor.ChangeoSchema

Bases: object

Change-O to Receptor mappings

fields = ['SEQUENCE_ID', 'SEQUENCE_INPUT', 'SEQUENCE_AA_INPUT', 'FUNCTIONAL', 'IN_FRAME', 'STOP', 'MUTATED_INVARIANT', 'INDELS', 'V_FRAMESHIFT', 'LOCUS', 'V_CALL', 'D_CALL', 'J_CALL', 'C_CALL', 'SEQUENCE_VDJ', 'SEQUENCE_IMGT', 'SEQUENCE_AA_VDJ', 'SEQUENCE_AA_IMGT', 'V_SEQ_START', 'V_SEQ_LENGTH', 'V_GERM_START_VDJ', 'V_GERM_LENGTH_VDJ', 'V_GERM_START_IMGT', 'V_GERM_LENGTH_IMGT', 'V_SEQ_AA_START', 'V_SEQ_AA_LENGTH', 'V_GERM_AA_START_VDJ', 'V_GERM_AA_LENGTH_VDJ', 'V_GERM_AA_START_IMGT', 'V_GERM_AA_LENGTH_IMGT', 'NP1_LENGTH', 'NP1_AA_LENGTH', 'D_SEQ_START', 'D_SEQ_LENGTH', 'D_GERM_START', 'D_GERM_LENGTH', 'D_SEQ_AA_START', 'D_SEQ_AA_LENGTH', 'D_GERM_AA_START', 'D_GERM_AA_LENGTH', 'NP2_LENGTH', 'NP2_AA_LENGTH', 'J_SEQ_START', 'J_SEQ_LENGTH', 'J_GERM_START', 'J_GERM_LENGTH', 'J_SEQ_AA_START', 'J_SEQ_AA_LENGTH', 'J_GERM_AA_START', 'J_GERM_AA_LENGTH', 'JUNCTION', 'JUNCTION_LENGTH', 'GERMLINE_IMGT', 'GERMLINE_AA_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', 'FWR1_AA_IMGT', 'FWR2_AA_IMGT', 'FWR3_AA_IMGT', 'FWR4_AA_IMGT', 'CDR1_AA_IMGT', 'CDR2_AA_IMGT', 'CDR3_AA_IMGT', 'N1_LENGTH', 'N2_LENGTH', 'P3V_LENGTH', 'P5D_LENGTH', 'P3D_LENGTH', 'P5J_LENGTH', 'D_FRAME', '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'
required = ['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.ChangeoSchemaAA

Bases: changeo.Receptor.ChangeoSchema

Change-O to Receptor amino acid mappings

required = ['SEQUENCE_ID', 'SEQUENCE_AA_INPUT', 'STOP', 'INDELS', 'LOCUS', 'V_CALL', 'SEQUENCE_AA_VDJ', 'SEQUENCE_AA_IMGT', 'V_SEQ_AA_START', 'V_SEQ_AA_LENGTH', 'V_GERM_AA_START_VDJ', 'V_GERM_AA_LENGTH_VDJ', 'V_GERM_AA_START_IMGT', 'V_GERM_AA_LENGTH_IMGT', 'GERMLINE_AA_IMGT']
class changeo.Receptor.Receptor(data)

Bases: object

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

property d_germ_aa_end

Position of the last amino acid in the D germline amino acid alignment

property d_germ_end

Position of the last nucleotide in the D germline sequence alignment

property d_seq_aa_end

Position of the last D amino acid in the input amino acid sequence

property 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

property j_germ_aa_end

Position of the last amino acid in the J germline amino acid alignment

property j_germ_end

Position of the last nucleotide in the J germline sequence alignment

property j_seq_aa_end

Position of the last J amino acid in the input amino sequence

property j_seq_end

Position of the last J nucleotide in the input sequence

property 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

property v_germ_aa_end_imgt

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

property v_germ_aa_end_vdj

Position of the last nucleotide in the ungapped V germline sequence alignment

property v_germ_end_imgt

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

property v_germ_end_vdj

Position of the last nucleotide in the ungapped V germline sequence alignment

property v_seq_aa_end

Position of the last V nucleotide in the input sequence

property 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

v_frameshift

whether the V segment contains a frameshift

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

sequence_aa_input

input amino acid sequence.

Type

Bio.Seq.Seq

sequence_aa_vdj

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

Type

Bio.Seq.Seq

sequence_aa_imgt

IMGT-gapped V(D)J amino 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

germline_aa_vdj

full ungapped germline V(D)J amino acid sequence.

Type

Bio.Seq.Seq

germline_aa_imgt

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

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

v_seq_aa_start

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

Type

int

v_seq_aa_length

number of V amino acid in the amino acid input sequence.

Type

int

v_germ_aa_start_imgt

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

Type

int

v_germ_aa_length_imgt

length of the IMGT numbered germline V amino acid alignment.

Type

int

v_germ_aa_start_vdj

position of the first amino acid in ungapped V germline amino acid alignment (1-based).

Type

int

v_germ_aa_length_vdj

length of the ungapped germline V amino acid 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

np1_aa_start

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

Type

int

np1_aa_length

number of untemplated amino acids 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

d_seq_aa_start

position of the first D amino acid in the input amino acidsequence (1-based).

Type

int

d_seq_aa_length

number of D amino acids in the input amino acid sequence.

Type

int

d_germ_aa_start

position of the first amino acid in D germline amino acid alignment (1-based).

Type

int

d_germ_aa_length

length of the germline D amino acid 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

np2_aa_start

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

Type

int

np2_aa_length

number of untemplated amino acid 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

j_seq_aa_start

position of the first J amino acid in the input amino acidsequence (1-based).

Type

int

j_seq_aa_length

number of J amino acid in the input amino acidsequence.

Type

int

j_germ_aa_start

position of the first amino acid in J germline amino acid alignment (1-based).

Type

int

j_germ_aa_length

length of the germline J amino acid 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

fwr1_aa_imgt

IMGT-gapped FWR1 amino acid sequence.

Type

Bio.Seq.Seq

fwr2_aa_imgt

IMGT-gapped FWR2 amino acid sequence.

Type

Bio.Seq.Seq

fwr3_aa_imgt

IMGT-gapped FWR3 amino acid sequence.

Type

Bio.Seq.Seq

fwr4_aa_imgt

IMGT-gapped FWR4 amino acid sequence.

Type

Bio.Seq.Seq

cdr1_aa_imgt

IMGT-gapped CDR1 amino acid sequence.

Type

Bio.Seq.Seq

cdr2_aa_imgt

IMGT-gapped CDR2 amino acid sequence.

Type

Bio.Seq.Seq

cdr3_aa_imgt

IMGT-gapped CDR3 amino acid sequence.

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_germ_aa_end': ('d_germ_aa_start', 'd_germ_aa_length'), 'd_germ_end': ('d_germ_start', 'd_germ_length'), 'd_seq_aa_end': ('d_seq_aa_start', 'd_seq_aa_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_germ_aa_end': ('j_germ_aa_start', 'j_germ_aa_length'), 'j_germ_end': ('j_germ_start', 'j_germ_length'), 'j_seq_aa_end': ('j_seq_aa_start', 'j_seq_aa_length'), 'j_seq_end': ('j_seq_start', 'j_seq_length'), 'junction_end': ('junction_start', 'junction_length'), 'v_alignment_aa_end': ('v_alignment_aa_start', 'v_alignment_aa_length'), 'v_alignment_end': ('v_alignment_start', 'v_alignment_length'), 'v_germ_aa_end_imgt': ('v_germ_aa_start_imgt', 'v_germ_aa_length_imgt'), 'v_germ_aa_end_vdj': ('v_germ_aa_start_vdj', 'v_germ_aa_length_vdj'), '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_aa_end': ('v_seq_aa_start', 'v_seq_aa_length'), '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_germ_aa_length': ('d_germ_aa_start', 'd_germ_aa_end'), 'd_germ_length': ('d_germ_start', 'd_germ_end'), 'd_seq_aa_length': ('d_seq_aa_start', 'd_seq_aa_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_germ_aa_length': ('j_germ_aa_start', 'j_germ_aa_end'), 'j_germ_length': ('j_germ_start', 'j_germ_end'), 'j_seq_aa_length': ('j_seq_aa_start', 'j_seq_aa_end'), 'j_seq_length': ('j_seq_start', 'j_seq_end'), 'junction_length': ('junction_start', 'junction_end'), 'v_alignment_aa_length': ('v_alignment_aa_start', 'v_alignment_aa_end'), 'v_alignment_length': ('v_alignment_start', 'v_alignment_end'), 'v_germ_aa_length_imgt': ('v_germ_aa_start_imgt', 'v_germ_aa_end_imgt'), 'v_germ_aa_length_vdj': ('v_germ_aa_start_vdj', 'v_germ_aa_end_vdj'), '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_aa_length': ('v_seq_aa_start', 'v_seq_aa_end'), 'v_seq_length': ('v_seq_start', 'v_seq_end')}
static logical(v, deparse=False)
static nucleotide(v, deparse=False)
parsers = {'c_call': 'identity', 'cdr1_aa_imgt': 'aminoacid', 'cdr1_imgt': 'nucleotide', 'cdr2_aa_imgt': 'aminoacid', 'cdr2_imgt': 'nucleotide', 'cdr3_aa_imgt': 'aminoacid', '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_aa_length': 'integer', 'd_germ_aa_start': 'integer', 'd_germ_length': 'integer', 'd_germ_start': 'integer', 'd_identity': 'double', 'd_score': 'double', 'd_seq_aa_length': 'integer', 'd_seq_aa_start': 'integer', 'd_seq_length': 'integer', 'd_seq_start': 'integer', 'dupcount': 'integer', 'functional': 'logical', 'fwr1_aa_imgt': 'aminoacid', 'fwr1_imgt': 'nucleotide', 'fwr2_aa_imgt': 'aminoacid', 'fwr2_imgt': 'nucleotide', 'fwr3_aa_imgt': 'aminoacid', 'fwr3_imgt': 'nucleotide', 'fwr4_aa_imgt': 'aminoacid', 'fwr4_imgt': 'nucleotide', 'germline_aa_imgt': 'aminoacid', 'germline_aa_vdj': 'aminoacid', '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_aa_length': 'integer', 'j_germ_aa_start': 'integer', 'j_germ_length': 'integer', 'j_germ_start': 'integer', 'j_identity': 'double', 'j_score': 'double', 'j_seq_aa_length': 'integer', 'j_seq_aa_start': 'integer', '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_aa_length': 'integer', 'np1_aa_start': 'integer', 'np1_length': 'integer', 'np1_start': 'integer', 'np2_aa_length': 'integer', 'np2_aa_start': 'integer', 'np2_length': 'integer', 'np2_start': 'integer', 'p3d_length': 'integer', 'p3v_length': 'integer', 'p5d_length': 'integer', 'p5j_length': 'integer', 'rev_comp': 'logical', 'sequence_aa_imgt': 'aminoacid', 'sequence_aa_input': 'aminoacid', 'sequence_aa_vdj': 'aminoacid', '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_frameshift': 'logical', 'v_germ_aa_length_imgt': 'integer', 'v_germ_aa_length_vdj': 'integer', 'v_germ_aa_start_imgt': 'integer', 'v_germ_aa_start_vdj': 'integer', '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_aa_length': 'integer', 'v_seq_aa_start': 'integer', '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_germ_aa_start': ('d_germ_aa_length', 'd_germ_aa_end'), 'd_germ_start': ('d_germ_length', 'd_germ_end'), 'd_seq_aa_start': ('d_seq_aa_length', 'd_seq_aa_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_germ_aa_start': ('j_germ_aa_length', 'j_germ_aa_end'), 'j_germ_start': ('j_germ_length', 'j_germ_end'), 'j_seq_aa_start': ('j_seq_aa_length', 'j_seq_aa_end'), 'j_seq_start': ('j_seq_length', 'j_seq_end'), 'junction_start': ('junction_length', 'junction_end'), 'v_alignment_aa_start': ('v_alignment_aa_length', 'v_alignment_aa_end'), 'v_alignment_start': ('v_alignment_length', 'v_alignment_end'), 'v_germ_aa_start_imgt': ('v_germ_aa_length_imgt', 'v_germ_aa_end_imgt'), 'v_germ_aa_start_vdj': ('v_germ_aa_length_vdj', 'v_germ_aa_end_vdj'), '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_aa_start': ('v_seq_aa_length', 'v_seq_aa_end'), 'v_seq_start': ('v_seq_length', 'v_seq_end')}