Releases: aineniamh/squirrel
Squirrel v1.0.12
Release notes
-
APOBEC3-reconstruction tree figure customisation. Occasionally, you may want to adjust the final APOBEC3-reconstruction tree figure output. There are now a number of options to help you achieve this. Firstly, rather than having to rerun the entire analysis, there is now an option that allows the user to re-render the tree figure only (
-tfig/--tree-figure-only
). The user must supply a tree file and matching branch reconstruction file that has been output by a previous squirrel run. This can be done with the-brf/--branch-reconstruction-file
and-tf/--tree-file
arguments. -
Alongside these files, the user can then specify a custom height (
--fig-height
) or width (--fig-width
) for the final tree vizualisation. -
The user may now also specify whether the reconstructed mutations vizualised on the branch are either represented by a
circle
hovering over the branch or asquare
spanning the branch with the--point-style
argument, and whether they want the points to begin stacking from theleft
orright
with--point-justify
. -
Adding in reference column in absence of bed file formats accepting a notes column.
-
Updating gene boundary files to have record of accession number in.
-
Squirrel now offers a sequence-specific mask option for making particular sites in a problematic sequence, rather than masking out the entire column across the alignment. This can be achieved with
--sequence-mask
and requires the user to supply a csv file with asequence
column that contains the sequence name (must match an id in the supplied FASTA file) and asite
column, with a 1-based position to mask. If a sequence needs multiple sites masked, specify them on separate lines in the file with the same sequence name. -
fix for issue #53 when a file is forgotten to be supplied, exits with handling
-
adding additional flag to either write binary mask file for beast or now an optoin to sep out dimers with a 0,1,2 mask string.
Squirrel v1.0.11
Release notes
- Fix to exclude file parsing and print out
- Fix to gene boundary parsing to match iqtree 1-base site reconstruction
- Only flag sites if most common base, aside from N or -, in qc mode
- Removing mako version pin
- Additional number of sites to mask
Squirrel v1.0.10
Release notes
- Resolving issue with outfile flag described in #41
- Making png of tree not transparent for better view in night mode
Squirrel v1.0.9
Release notes
- Update to squirrel for identifying root node name to deal with issue #32
- Small mod to background annotations
Squirrel v1.0.8
- Separates out APOBEC3 reconstruction from the main phylogenetic pipeline so it can be run optionally with
--run-apobec3-phylo
- Add option to provide additional background sequences as a separate FASTA with
-bf FASTA
if using--include-background
option.
What's Changed
- Report dev by @aineniamh in #23
- Phylo custom dev by @aineniamh in #26
- Minor updates to README and command help text by @rmcolq in #27
Full Changelog: 1.0.7...1.0.8
Squirrel v1.0.7
Merge pull request #21 from aineniamh/dev Small fix to tree svg path, small mod to Dockerfile
Squirrel v1.0.6
Release notes
- Squirrel now outputs a HTML report
- additional pip dependency (mako==1.2)
Squirrel v1.0.5
Release notes
- Updating squirrel to now include additional flag:
-bg, --include-background
Include a default background set of sequences for the phylogenetics pipeline. The set will be determined by the `--clade` specified.
- Outgroups do not need to be specified with
--include-background
mode. - Valid clade names are now cladei, cladeia, cladeib, cladeii, cladeiia and cladeiib
--clade CLADE Specify whether the alignment is primarily for `cladei` or `cladeii` (can also specify a or b, e.g. `cladeia`, `cladeiib`). This will determine reference used for alignment, mask file and background set
used if `--include-background` flag used in conjunction with the `--run-phylo` option. Default: `cladeii`
- Additional updates fixes iqtree output directory within squirrel and only final tree and state files are written to outdir, rest now temp.
Squirrel v1.0.4
Minor version bump to fix matplotlib warning which appears on some OS
Squirrel v1.0.3
Version bump - no changes