Squirrel v1.3.2

Release notes

• Clade option now includes panclade
• Adding in pan clade composite consensus reference generated from an alignment of PX667572 and NC_063383.
• The gene boundaries file for pan clade contains genes from clade I and clade II with coordinates mapped from the original reference sequence to the pan clade coordinate system
• The ITR is trimmed from 193610, which is the ITR mask site for clade II mapped onto the new coordinate system
• The mask file is currently empty
• Some translation functions are included that can generate the coordinate system map (in utils/panclade_map.py). To access the coordinate map run the following:

import squirrel.utils.panclade_map as pm
coordinates = pm.get_coordinate_map()

• This function extracts coordinate mappings from predefined CIGAR strings. Retrieves a dictionary of CIGAR strings for reference sequences and converts each CIGAR string into bidirectional coordinate mappings between genomic and alignment positions. It returns a dict: Dictionary mapping sequence IDs to coordinate information dictionaries, each containing:
  • cigar (str): CIGAR string representation.
  • genome_to_aln (dict): Maps genome positions to alignment positions.
  • aln_to_genome (dict): Maps alignment positions to genome positions,
    with None for gap positions.

Squirrel v1.3.1

Release notes

Patch release with iqtree3 executable called now, and env file wanting iqtree >=3.0 to be installed.

Squirrel v1.3

Release notes

• For tree annotation, A3/non-A3 proportion now reported per branch as well as per subtree
• Rework python packaging, migrating to pyproject.toml file
• Rework how data packaging done within project, now uses importlib.resources
• Some dependencies updated, including snakemake-minimal, which is now pinned to >=9.9.0. This is post API removal in snakemake, which meant the pipeline call is reworked and the custom logging is no longer easily done. Consequences of this mean that more snakemake logging to screen during the run, and that any sub-pipelines that are run within a pipeline are also printed to screen. More 'noise', but it might actually make debugging easier, and I personally love seeing loads of text fly by when it's running.
• Dependencies changed:
  • python=3.10 -> python>=3.10
  • snakemake-minimal=7.32 -> snakemake-minimal>=9.9.0
• Re-introduction of mac-os actions, which now run with the updated dependencies (I'm guessing snakemake was what was braking it before, not much else has changed).
• Check for special characters in input sequence names (issues #82 and #69). Prints informative error describing what characters are in what sequence ids and exits.
• Check if entire sequence is just Ns. If all input sequences are just N, will exit with an error (#50)
• Can now accept a pre-computed tree (but requires statefile and alignment too) as per request #62 from PR #84. This change will allow users to supply a tree, however if multiple likelihood annotations are on the tree, the graphic will not render as baltic fails to load it
• Updating executable call for iqtree -> iqtree2 (issue #73)

Squirrel v1.2.2

Release notes

• Patch for division by 0 so figtree can handle gradient shading

Squirrel v1.2.1

Release notes

• Annotated tree output now
• APOBEC3 counts, non-APO counts, proportion, binomial probability based on 11% background distribution
• Same for each branch, and each subtree below each branch

Squirrel v1.2

Release notes

• Update to squirrel --clade split functionality with squirrel now using a custom pangoLEARN RF model for MPXV clade assignment
• Fix bug where fig width and height flags were switched
• Outgroup issues no longer reported in seq-qc output
• Fixing id in html report when multiple clades reported

Squirrel v1.1.7

Release notes

• Adding extra flag for path in epi2me report

Squirrel v1.1.6

Handling some additional edge cases where no sequences successfully get assigned a clade in 'split' clade mode.

Squirrel v1.1.5

Release notes

• Modifying check for duplicate entry- if background added, check if outgroup included before adding and running dup check

Squirrel v1.1.4

Release notes

• in report making section, check if clades assigned greater than 1, then use the string to configure the outfile name rather than looking for clade alone
• check in outgroup adding if include background also used, and dont break if duplicate name- could already be added in the background part
• removing redundant directory stems as outfile contains path already