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

Dev ref genome validator #74

Merged
merged 67 commits into from
Sep 20, 2024
Merged

Dev ref genome validator #74

merged 67 commits into from
Sep 20, 2024

Conversation

nsheff
Copy link
Member

@nsheff nsheff commented Sep 3, 2024

No description provided.

@donaldcampbelljr
initial work towards ref genome prediction and validation
27a6ddd
@donaldcampbelljr
initial commit for pulling and caching 1000 bedfiles
e2c6502
@donaldcampbelljr
add beginnings of excluded_ranges overlap processing
8e90842
@donaldcampbelljr
add subprocess execution and output checking
e88d019
@donaldcampbelljr
working example for excluded ranges processing
2d027b2
@donaldcampbelljr
some polish, use getattr
9d17108
@donaldcampbelljr
add stats analysis script, creating heatmap
c3bd066
@donaldcampbelljr
adjust heatmap, add example output
4b8f94b
@donaldcampbelljr
update to use more bins when producing heatmap
722ec92
@donaldcampbelljr
sort via column mean
abc0d42
@donaldcampbelljr
wrap sample accessing via Geofetch in try except, only pull file list
9d1314e
@donaldcampbelljr
add sorting for heatmap columns, truncate names for readability, atte…
d8401e9 
…mpt adding clustermaps
@donaldcampbelljr
change to number of hits
7462d30
@donaldcampbelljr
add getting chrom sizes for bed file and doing a comparison with refg…
2ee7594 
…enome chrom sizes
nsheff
nsheff commented Sep 3, 2024
View reviewed changes
@donaldcampbelljr donaldcampbelljr marked this pull request as draft September 4, 2024 14:12
donaldcampbelljr and others added 25 commits September 11, 2024 09:58
@donaldcampbelljr
fix filtering by column values
5e05cbb
@donaldcampbelljr
work towards new stats graphs for smaller subset of beds
7631af6
@donaldcampbelljr
add creation of heatmap from smaller dataset
5634eae
@donaldcampbelljr
add ncbi, ensembl chrom sizes and genome models
fcd80fc
@donaldcampbelljr
add simple counting chrom.sizes duplicates
4794508
@donaldcampbelljr
redo heatmap 4 discrete colors
bc05a2c
@donaldcampbelljr
light refactoring
5c8835a
@donaldcampbelljr
refactor chrom.sizes locales
8a3e913
@donaldcampbelljr
refactor chrom.sizes locales, add default genomemodel func
ea85fbd
@khoroshevskyi
refactoring
156376b
@khoroshevskyi
added concise to ref gen validator return
85f449e
@khoroshevskyi
added better opening of the bed file
1ada5c9
@donaldcampbelljr
fix stats scripts after refactor
e8be1fe
@donaldcampbelljr
fix row skipping during file opening
ccf0c5c
@donaldcampbelljr
fix logic for q_and_not_m > 0:
cce5dcc
@donaldcampbelljr
add mm39 to stats comparison
8677629
@donaldcampbelljr
fix geotfetch portion of validator script
1b0c4ef
@donaldcampbelljr
add bedfile read exception
171a685
@donaldcampbelljr
add valueerror exception
1591178
@khoroshevskyi
moved opening bed file to geniml
0490dd1
@donaldcampbelljr
fix refactoring to main from refgenomevalidator.py
36ddbef
@khoroshevskyi
cleaning docstrings
cbe02f4
@khoroshevskyi
version and typos
50f65e0
@khoroshevskyi
Merge pull request #77 from databio/ref_validator_refactoring
e34e4af 
Ref validator refactoring
@khoroshevskyi
Merge branch 'dev' into dev_ref_genome_validator
8c1c2d3
@khoroshevskyi khoroshevskyi self-requested a review September 19, 2024 17:02
@khoroshevskyi khoroshevskyi merged commit f40682d into dev Sep 20, 2024
1 of 3 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@khoroshevskyi khoroshevskyi Awaiting requested review from khoroshevskyi

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

Successfully merging this pull request may close these issues.
3 participants
@nsheff @khoroshevskyi @donaldcampbelljr