changeo.Receptor

Receptor data structure

class changeo.Receptor.AIRRSchema

Bases: object

AIRR format to Receptor mappings

custom_fields = ['c_call', 'locus', '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_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', 'clone_id', 'cell_id']
fields = ['sequence_id', 'sequence', 'sequence_alignment', 'germline_alignment', 'rev_comp', 'productive', 'stop_codon', 'vj_in_frame', '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', 'locus', '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_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', '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', '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 = ['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', 'CDR3_IGBLAST', 'CDR3_IGBLAST_AA', 'CONSCOUNT', 'DUPCOUNT', 'CLONE', 'CELL']
fields = ['SEQUENCE_ID', 'SEQUENCE_INPUT', 'FUNCTIONAL', 'IN_FRAME', 'STOP', 'MUTATED_INVARIANT', 'INDELS', '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', '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', 'CDR3_IGBLAST', 'CDR3_IGBLAST_AA', 'CONSCOUNT', 'DUPCOUNT', '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', '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.

junction_start

position of the first 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

str – unique sequence identifier.

rev_comp

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

functional

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

in_frame

bool – whether junction region is in-frame.

stop

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

mutated_invariant

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

indels

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

sequence_input

Bio.Seq.Seq – input nucleotide sequence.

sequence_vdj

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

sequence_imgt

Bio.Seq.Seq – IMGT-gapped V(D)J nucleotide sequence.

junction

Bio.Seq.Seq – ungapped junction region nucletide sequence.

junction_aa

Bio.Seq.Seq – ungapped junction region amino acid sequence.

junction_length

int – length of the junction in nucleotides.

germline_vdj

Bio.Seq.Seq – full ungapped germline V(D)J nucleotide sequence.

germline_vdj_d_mask

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

germline_imgt

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

germline_imgt_d_mask

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

v_call

str – V allele assignment(s).

d_call

str – D allele assignment(s).

j_call

str – J allele assignment(s).

c_call

str – C region assignment.

v_seq_start

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

v_seq_length

int – number of V nucleotides in the input sequence.

v_germ_start_imgt

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

v_germ_length_imgt

int – length of the IMGT numbered germline V alignment.

v_germ_start_vdj

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

v_germ_length_vdj

int – length of the ungapped germline V alignment.

np1_start

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

np1_length

int – number of untemplated nucleotides between the V and D segments.

d_seq_start

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

d_seq_length

int – number of D nucleotides in the input sequence.

d_germ_start

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

d_germ_length

int – length of the germline D alignment.

np2_start

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

np2_length

int – number of untemplated nucleotides between the D and J segments.

j_seq_start

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

j_seq_length

int – number of J nucleotides in the input sequence.

j_germ_start

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

j_germ_length

int – length of the germline J alignment.

v_score

float – alignment score for the V.

v_identity

float – alignment identity for the V.

v_evalue

float – E-value for the alignment of the V.

v_btop

str – BTOP for the alignment of the V.

v_cigar

str – CIGAR for the alignment of the V.

d_score

float – alignment score for the D.

d_identity

float – alignment identity for the D.

d_evalue

float – E-value for the alignment of the D.

d_btop

str – BTOP for the alignment of the D.

d_cigar

str – CIGAR for the alignment of the D.

j_score

float – alignment score for the J.

j_identity

float – alignment identity for the J.

j_evalue

float – E-value for the alignment of the J.

j_btop

str – BTOP for the alignment of the J.

j_cigar

str – CIGAR for the alignment of the J.

vdj_score

float – alignment score for the V(D)J.

fwr1_imgt

Bio.Seq.Seq – IMGT-gapped FWR1 nucleotide sequence.

fwr2_imgt

Bio.Seq.Seq – IMGT-gapped FWR2 nucleotide sequence.

fwr3_imgt

Bio.Seq.Seq – IMGT-gapped FWR3 nucleotide sequence.

fwr4_imgt

Bio.Seq.Seq – IMGT-gapped FWR4 nucleotide sequence.

cdr1_imgt

Bio.Seq.Seq – IMGT-gapped CDR1 nucleotide sequence.

cdr2_imgt

Bio.Seq.Seq – IMGT-gapped CDR2 nucleotide sequence.

cdr3_imgt

Bio.Seq.Seq – IMGT-gapped CDR3 nucleotide sequence.

cdr3_igblast

Bio.Seq.Seq – CDR3 nucleotide sequence assigned by IgBLAST.

cdr3_igblast_aa

Bio.Seq.Seq – CDR3 amino acid sequence assigned by IgBLAST.

n1_length

int – M nucleotides 5’ of the D segment.

n2_length

int – nucleotides 3’ of the D segment.

p3v_length

int – palindromic nucleotides 3’ of the V segment.

p5d_length

int – palindromic nucleotides 5’ of the D segment.

p3d_length

int – palindromic nucleotides 3’ of the D segment.

p5j_length

int – palindromic nucleotides 5’ of the J segment.

d_frame

int – D segment reading frame.

conscount

int – number of reads contributing to the UMI consensus sequence.

dupcount

int – copy number of the sequence.

clone

str – clonal cluster identifier.

cell

str – origin cell identifier.

annotations

dict – dictionary containing all unknown fields.

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'), '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'), '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', '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', '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'), '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')}