abtools.phylogeny: Phylogenetic analysis of antibody lineages

abtools._phylogeny.run(**kwargs)

Builds a phylogenetic representation of antibody sequences.

output is required, as well as one of input, alignment or newick.

Parameters:
  • input (str) –

    Can be one of three things:

    1. Path to a FASTA-formatted file containing input sequences.
    2. A list of AbTools Sequence objects.
    3. A list of dictionaries, containing at minimum name_key and seq_key.
  • output (str) – Path to the output directory, into which tree images and all intermediate files will be deposited.
  • root (str) – Path to a FASTA-formatted file containing a single sequence which will be used to root the tree. If not provided, tree will be unrooted.
  • mabs (str) – Path to a FASTA-formatted file containing mAb sequences. If supplying both mAb sequences and NGS sequences, passing the mAb sequences separately allows you to modify their representation separately (for example, show sequence IDs for just the mAb sequences).
  • alignment (str) – Path to a multiple sequence alignment, in FASTA format. If sequences are already aligned, this will save some computational time since the alignment will not be redone.
  • newick (str) – Path to a tree file, in Newick format. As with alignment, this is primarily to save computational time if the tree file has already been generated.
  • name_key (str) – If input is a list of Sequence objects or dicts, this key will be used to find the sequence ID. Default is seq_id.
  • sequence_key (str) – If input is a list of Sequence objects or dicts, this key will be used to find the sequence. Default is vdj_nt.
  • timepoints (str) –

    Path to a Tab-delimited file, of the following format (one per line):

    TimepointName    TimepointOrder    TimepointColor

    TimepointName should prepended to the sequences in the input file (separated by delimiter).

    TimepointOrder is an integer that indicates the order in which the timepoints should be sorted.

    TimepointColor is a hex value that will be used to color the phylogenetic tree. If mAb sequences are provided, the ‘mab’ TimepointName will be used to sort/color the mAb sequences. If not provided, colors will be automatically selected and timepoints will be determined by a simple sort of the raw timepoint values parsed from the input file.

  • is_aa (bool) – If True, input sequences will be assumed to be amino acid sequences. Default is False, which assumes nucleotide sequences.
  • delimiter (str) – The delimiter used in sequence IDs to separate the timepoint from the sequence name. Default is _.
  • scale (int) – Horizontal scale of the phylogeny. Default is None, which uses the default ete2 value.
  • branch_vertical_margin (float) – Vertical scale of the phylogeny. Default is None, which uses the default ete2 value.
  • label_nodes (str) – Type of nodes to be labeled. Options are: all, none, no-root, mab, input, and root.
  • label_fontsize (float) – Font size for the node labels.
  • tree_orientation (int) – If 0, tree is drawn from left to right. If 1, tree will be drawn from right to left (mirror). Default is 0.