Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

WIP: Add jcvi.graphics.ribbon module #733

Merged
merged 50 commits into from
Dec 26, 2024
Merged

WIP: Add jcvi.graphics.ribbon module #733

merged 50 commits into from
Dec 26, 2024

Conversation

Adamtaranto
Copy link
Collaborator

@Adamtaranto Adamtaranto commented Dec 25, 2024 •
edited
Loading

When complete, this PR will add a new module jcvi.graphic.ribbon which is derived from the synteny module.

Closes #724

Ribbon adds support for plotting whole genome alignments instead of linked orthologous genes.

  • Set contig orientation
  • Set contig zoom interval
  • Manually set ribbon colours
  • Convert LASTZ to ribbon link format
  • Set annotation track offsets
  • Set annotation track colours
  • Add tests for processing new config format
  • Use base logger

@Adamtaranto
Initialise dev branch
8178517
@Adamtaranto
Merge branch 'master' into dev
08b1110
@Adamtaranto
Merge branch 'master' into dev
3b53422
@Adamtaranto
Do not plot blocks/ribbons from lines beginning with *
f711d54
@Adamtaranto
Add opt noline to suppress ribbon outlines
20822ff
@Adamtaranto
Merge branch 'master' into dev
a6481dc
@Adamtaranto
Port style option for straight ribbons + various formating fixes
29845fc
@Adamtaranto
Port xrange to Py3 and fix default strand colour selection
a052c78
@Adamtaranto
Merge branch 'master' into dev
33f915d
@Adamtaranto
Merge branch 'master' into dev
cef3130
@Adamtaranto
Migrate Ribbon scripts to py3
88bed6a
@Adamtaranto
Beta support for PAF input
40ae6b7
@Adamtaranto
pep8 fixes
90ac8b7
@Adamtaranto
Merge branch 'master' into dev
da8113d
@Adamtaranto
Merge branch 'master' into dev
333fc2e
@Adamtaranto
Black formatting
65057ad
@Adamtaranto
Merge branch 'master' into dev
6c6da04
@Adamtaranto
add ribbon test case files
9a0cf01
@Adamtaranto
log matplotlib backend
37ea56b
@Adamtaranto
add logging to ribbon
b265c46
@Adamtaranto
Merge branch 'dev' of github.com:Adamtaranto/jcvi into dev
e36ab91
@Adamtaranto
Merge branch 'master' into dev
b4a44fb
@Adamtaranto
Do not try to set usetex=False or resave
8e4c872 
if savefig fails. Instead just return error msg.
@Adamtaranto
Replace check_call with check_out in sh()
8029175 
Allows collection of outputs.
Added redirect_error arg so stderr can be
redirected to stdout and user in error logging.
@Adamtaranto
Collect stderr msgs from lastal for use in
a5225ec 
informative logging.
@Adamtaranto
Log suggestion to use --notex if savefig fails
3f7ad6d
@Adamtaranto
Merge branch 'master' into dev
7abd51e
@Adamtaranto
Add cleanup empty pdf before exit if savefig fails
00ff793
@Adamtaranto
Merge branch 'main' of https://github.com/tanghaibao/jcvi
6b986bb
@Adamtaranto
Merge branch 'master' into dev
2dc790c
tanghaibao
tanghaibao reviewed Dec 25, 2024
View reviewed changes
Copy link
Owner

@tanghaibao tanghaibao left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks great and thanks for adding this module. Some minor comments then we should be able to merge.

jcvi/graphics/base.py Show resolved Hide resolved
jcvi/graphics/ribbon.py Outdated Show resolved Hide resolved
temp/ribbon_testing/data/3S_genes.bed Outdated Show resolved Hide resolved
@Adamtaranto
Copy link
Collaborator Author

Note: Black formatter action seems to fail when PR is not owned by tanghaibao/jcvi.

Need to look into this.

@tanghaibao tanghaibao merged commit 0a5b1f3 into tanghaibao:main Dec 26, 2024
5 checks passed
@Adamtaranto Adamtaranto mentioned this pull request Dec 26, 2024
Open
2 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@tanghaibao tanghaibao tanghaibao approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Support custom alignment blocks in Microsynteny plots
2 participants
@Adamtaranto @tanghaibao