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V2 #72

Merged
merged 71 commits into from
Aug 22, 2024
Merged

V2 #72

merged 71 commits into from
Aug 22, 2024

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babayagaofficial
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@babayagaofficial babayagaofficial commented Aug 15, 2024 •
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Still to do:

babayagaofficial and others added 24 commits June 18, 2024 10:57
@babayagaofficial
Allow for both linear and circular plasmids, as well as regions (alth…
109bde6 
…ough regions with caveats: assume embedded into circular genome, and that they are all oriented 'correctly', as two regions that are the same, but one is the reverse of the other, will have DCJ distance 1 under current assumptions)
@babayagaofficial
Allow to skip integerisation. Containment network is still calculated…
bb7be20 
… from nucmer, like in anno workflow, but then DCJ is calculated from a provided unimog file (one entry per genome, i.e. not pairwise defined)
@babayagaofficial
Merge pull request #64 from iqbal-lab-org/skip_integerisation
e0ffec9 
Allow to skip integerisation
@babayagaofficial
Merge branch 'v2' into topology
ccc0bf8
@babayagaofficial
Remove integerisation from annotation workflow
699f522
@babayagaofficial
Remove anno options from run_pling.py
bcd53d7
@babayagaofficial
Remove --use-conda flag for running snakemake
ab7d602
@babayagaofficial
pip installablity via poetry package. does not handle mummer and glpk…
af771c6 
… dependency as these are not pypi packages
@babayagaofficial
changes to pyproject.toml to try get conda build instead of pypi build
27f2197
@babayagaofficial
Solution to distance between genome and reverse complemented genome: …
8b9972f 
…compare orientations of longest block on ref and query. If they're different, reverse the fake marker on the query sequence. If the longest blocks on ref and query are not the same, then the orientation is ambiguous and change nothing about the fake marker.
@babayagaofficial
Merge branch 'topology' of https://github.com/iqbal-lab-org/pling int…
5ab9ee3 
…o topology
@babayagaofficial
Merge pull request #62 from iqbal-lab-org/topology
22ea857 
Allow for both linear and circular plasmids, as well as regions
@babayagaofficial
Change flags in delta-filter. Fixes issue #57.
b44e943
@babayagaofficial
Mild refactoring
e09454c
@babayagaofficial
Refactored dcj calculation scripts and Snakefile to have less repeate…
4fe971e 
…d code, to make any future tweaking easier
@babayagaofficial
Installation via pip, removal of --use-conda related lines in Snakefi…
f09ace7 
…les, single yaml with all dependancies. Preparation for making conda installation work
@babayagaofficial
Remove defaults channel because anaconda is making a fuss about EBI u…
5ab5e0b 
…sing it
@babayagaofficial
Merge branch 'v2' into refactor
b32e3d5
@babayagaofficial
Merge pull request #69 from iqbal-lab-org/refactor
bfe8210 
Refactor
@babayagaofficial
Fixes some remaining conflicts from merging refactor branch into v2 b…
da3f79d 
…ranch
@babayagaofficial
Missing snakemake dependancy
66bcc38
@babayagaofficial
Set up to handle documentation via readthedocs
c25b544
@babayagaofficial
Update README.rst
4ab270d
@babayagaofficial
Merge branch 'main' of https://github.com/iqbal-lab-org/pling into v2
c4e72fd
babayagaofficial and others added 27 commits August 16, 2024 13:26
@babayagaofficial
Update ci.yaml
6a61d3c
@babayagaofficial
Updated Namespaces for tests
a4a147d
@babayagaofficial
Update unit tests
d8a8e7b
@babayagaofficial
Merge branch 'v2' of https://github.com/iqbal-lab-org/pling into v2
7697f54
@babayagaofficial
Update ci.yaml
64da567
@babayagaofficial
Update ci.yaml
1415ac7
@babayagaofficial
Update ci.yaml
32e56a2
@babayagaofficial
Update ci.yaml
73ff997
@babayagaofficial
Update ci.yaml
49d57b0
@babayagaofficial
Update ci.yaml
8a44c7d
@babayagaofficial
Update ci.yaml
f99c747
@babayagaofficial
Update ci.yaml
5d94a4f
@babayagaofficial
Update ci.yaml
3919b0d
@babayagaofficial
Don't load gurobi unless necessary
8f2c32c
@babayagaofficial
Merge branch 'v2' of https://github.com/iqbal-lab-org/pling into v2
c389042
@babayagaofficial
Not (less?) buggy load of gurobi as needed
7c89e34
@babayagaofficial
Remove remanants of annotation workflow
0356bd7
@babayagaofficial
Fix bugs in skip integerisation workflow
12c0149
@babayagaofficial
Update unittests to include skip workflow and to be findable via unit…
df741c3 
…test discover
@babayagaofficial
Forgot input unimog file for skip workflow unittest
534759a
@babayagaofficial
Updated advanced usage documentation
aa7635f
@babayagaofficial
Updated advanced usage documentation
818aabd
@babayagaofficial
Update basic usage
1f53283
@babayagaofficial
Json output options
a1b32c4
@babayagaofficial
Update unit test Namespaces
1af1447
@babayagaofficial
Update documentation
5577215
@babayagaofficial
Update documentation
f308ec0
@babayagaofficial
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With this version we solve issues: #63, #60, #57, #44 and #6; and partially address #73 and #67.

@babayagaofficial babayagaofficial merged commit 95a624d into main Aug 22, 2024
3 checks passed
@babayagaofficial babayagaofficial deleted the v2 branch August 29, 2024 15:37
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Successfully merging this pull request may close these issues.

Handling effects of setting containment_distance to 1
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@babayagaofficial