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Releases: aineniamh/squirrel

Squirrel v1.0.12

10 Nov 14:53
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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 a square spanning the branch with the --point-style argument, and whether they want the points to begin stacking from the left or right 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 a sequence column that contains the sequence name (must match an id in the supplied FASTA file) and a site 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

15 Oct 17:15
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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

20 Sep 17:41
5643499
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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

18 Sep 12:48
32c50f2
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Release notes

  • Update to squirrel for identifying root node name to deal with issue #32
  • Small mod to background annotations

Squirrel v1.0.8

26 Aug 10:05
8997730
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  • 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

Full Changelog: 1.0.7...1.0.8

Squirrel v1.0.7

22 Aug 20:46
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Merge pull request #21 from aineniamh/dev

Small fix to tree svg path, small mod to Dockerfile

Squirrel v1.0.6

22 Aug 17:26
2f0600e
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Release notes

  • Squirrel now outputs a HTML report
  • additional pip dependency (mako==1.2)

Squirrel v1.0.5

22 Aug 14:01
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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

20 Aug 21:13
493b685
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Minor version bump to fix matplotlib warning which appears on some OS

Squirrel v1.0.3

19 Aug 14:38
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Version bump - no changes