Clone and Lineage Tree Schema (Experimental)¶
A unique inferred clone object that has been constructed within a single data processing for a single repertoire and a subset of its sequences and/or rearrangements.
A clone object may have one or more inferred lineage trees. Each tree is represented by a Newick string for its edges and a dictionary of node objects.
File Format Specification¶
The file format has not been specified yet.
Clone Fields¶
Name |
Type |
Attributes |
Definition |
---|---|---|---|
|
string |
required, nullable |
Identifier for the clone. |
|
string |
optional, nullable |
Identifier to the associated repertoire in study metadata. |
|
string |
optional, nullable |
Identifier of the data processing object in the repertoire metadata for this clone. |
|
array of string |
optional, nullable |
List sequence_id strings that act as keys to the Rearrangement records for members of the clone. |
|
string |
optional, nullable |
V gene with allele of the inferred ancestral of the clone. For example, IGHV4-59*01. |
|
string |
optional, nullable |
D gene with allele of the inferred ancestor of the clone. For example, IGHD3-10*01. |
|
string |
optional, nullable |
J gene with allele of the inferred ancestor of the clone. For example, IGHJ4*02. |
|
string |
optional, nullable |
Nucleotide sequence for the junction region of the inferred ancestor of the clone, where the junction is defined as the CDR3 plus the two flanking conserved codons. |
|
string |
optional, nullable |
Amino acid translation of the junction. |
|
integer |
optional, nullable |
Number of nucleotides in the junction. |
|
integer |
optional, nullable |
Number of amino acids in junction_aa. |
|
string |
required, nullable |
Assembled, aligned, full-length inferred ancestor of the clone spanning the same region as the sequence_alignment field of nodes (typically the V(D)J region) and including the same set of corrections and spacers (if any). |
|
string |
optional, nullable |
Amino acid translation of germline_alignment. |
|
integer |
optional, nullable |
Start position in the V gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
|
integer |
optional, nullable |
End position in the V gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
|
integer |
optional, nullable |
Start position of the D gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
|
integer |
optional, nullable |
End position of the D gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
|
integer |
optional, nullable |
Start position of the J gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
|
integer |
optional, nullable |
End position of the J gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
|
integer |
optional, nullable |
Junction region start position in the alignment (1-based closed interval). |
|
integer |
optional, nullable |
Junction region end position in the alignment (1-based closed interval). |
|
integer |
optional, nullable |
Number of Rearrangement records (sequences) included in this clone |
|
string |
optional, nullable |
sequence_id of the seed sequence. Empty string (or null) if there is no seed sequence. |
Tree Fields¶
Name |
Type |
Attributes |
Definition |
---|---|---|---|
|
string |
required, nullable |
Identifier for the tree. |
|
string |
required, nullable |
Identifier for the clone. |
|
string |
required, nullable |
Newick string of the tree edges. |
|
object |
optional, nullable |
Dictionary of nodes in the tree, keyed by sequence_id string |
Node Fields¶
Name |
Type |
Attributes |
Definition |
---|---|---|---|
|
string |
required, nullable |
Identifier for this node that matches the identifier in the newick string and, where possible, the sequence_id in the source repertoire. |
|
string |
optional, nullable |
Nucleotide sequence of the node, aligned to the germline_alignment for this clone, including including any indel corrections or spacers. |
|
string |
optional, nullable |
Junction region nucleotide sequence for the node, where the junction is defined as the CDR3 plus the two flanking conserved codons. |
|
string |
optional, nullable |
Amino acid translation of the junction. |