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Expected refactoring (copied old PR by @golobor)#170

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nvictus merged 91 commits intomasterfrom
develop
Sep 9, 2020
Merged

Expected refactoring (copied old PR by @golobor)#170
nvictus merged 91 commits intomasterfrom
develop

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@mimakaev mimakaev commented Jun 30, 2020 •
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  • rename supports → regions
  • assign_supports:
    • bioframe intersect? Create a function that takes two sets of intervals, where the second is non-overlapping and sorted, and assigns the span of each set 1 interval in set 2 intervals. Make sure that it works with different resolutions, where spans of individual pixels may overflow chromosomal arms. Should end up in bioframe.
    • (kind of done with array options) rewrite assign_supports as a generic array operation on binspans?.. I.e. overlap a region and a point, but w/o chromosomes.
    • [x ] modify diagsums to use these new functions
  • bioframe.tools.split_chromosomes (Do we still need this?)
    • if centromere is missing, assume the split point at 0
    • Allow BED inputs
    • multiple split points per chromosome
  • clean up diag_assym
    • what’s this regions1, regions2?..
  • autogenerate transforms from weights?
  • [x ] in bioframe, set up an easy way to generate and retrieve chromosomal arms
  • [x ] (subject to change) finalize the format of the expected table
  • store data inside coolers

sergpolly and others added 30 commits May 3, 2019 16:51
@sergpolly
Merge pull request #4 from dekkerlab/master
fd91c25 
sync develop with master
@sergpolly
added initial dot-calling notebook
05748ef
@sergpolly
updated notebook
cd08bc0
@sergpolly
updated the dots notebook
956c5da
@sergpolly
updated notebook again
950d465
@sergpolly
before vacation notebook updates
f3928b3
@sergpolly
dot-calling notebook cleanup
b125e1c
@nvictus
Remove deprecated functions
ea21dba
@sergpolly
Merge pull request #8 from mirnylab/master
74c622a 
get latest from upstream
@sergpolly
Merge pull request #9 from mirnylab/master
9bff1ce 
Mock out imports directly so sphinx-click works (#136)
@mimakaev
added logbin_expected
e39c7c1
@mimakaev
split logbin_expected into two functions
bd52d3a
@mimakaev
improved logbins; added persistent logbins
dc7302a
@mimakaev
updated docs for logbin_expected; black
ec4acd5
@mimakaev
merge with upstream
20cd01b
@mimakaev
added black
192cd18
@golobor
expected: rename regions->supports
6ebb1b4
@golobor
common.py: add assign_regions_to_bins
c0e42db
@nvictus
Merge branch 'master' into develop
f413608
@nvictus
Merge branch 'master' into develop
b2b27f3
@golobor
expected.py: bugfix; rename diag->dist
379ab78
@Phlya
Allow regions in expected CLI (#146)
2851367 
* Make saddle strength work with NaNs

* Allow regions in CLI for expected

* Fix region_names without regions
@mimakaev
Merge branch 'master' of http://github.com/mirnylab/cooltools
d038b1e
@sergpolly @nvictus
@Phlya @mimakaev @itsameerkat
merge latest from master to develop (#155)
21cec77 
* More docstring edits

* Mock out imports directly

* Apply suggestions from code review

Co-Authored-By: Sergey Venev <sergpolly@gmail.com>

* Restore numpy to docs requirements

* Fix trans bad pixel counting

* fixed typo, added scalar extraction from array

* Update cooltools/expected.py

Co-Authored-By: Nezar Abdennur <nabdennur@gmail.com>

* Set default zoom order to 1

Somehow default zoom order was set to 3 instead of a much better default of 1! Goes against the docstring too.

* Change to new bioframe function names (#149)

* updated bioframe.slice_bedframe to bioframe.bedslice in line 337

* updated bioframe.bisect_bedframe to bioframe.bedbisect in line 356

* Update license

* Bump to dev version

* Revert changes to bioframe functions

* Pin dependency of cooltools 0.3 to bioframe 0.0

* Release v0.3.2

Co-authored-by: Nezar Abdennur <nabdennur@gmail.com>
Co-authored-by: Ilya Flyamer <flyamer@gmail.com>
Co-authored-by: Maksim Imakaev <mimakaev@gmail.com>
Co-authored-by: Sameer Abraham <sameer.abraham0@gmail.com>
@nvictus
Bump again to 0.4.0-dev
a129acf
@nvictus
Start using CliRunner for testing cli commands
32be1c5
@nvictus
Develop (#156)
34b4681 
* Bump again to 0.4.0-dev

* Start using CliRunner for testing cli commands
@sergpolly
Merge remote-tracking branch 'upstream/master'
cab2fb3
@sergpolly
Merge branch 'master' into develop
34034e6
@mimakaev
fixed saddle code to accept bedslice
2fbb2eb
sergpolly and others added 22 commits June 19, 2020 00:44
@sergpolly
Merge branch 'develop' of https://github.com/dekkerlab/cooltools into…
59d9129 
… develop
@mimakaev
cis eig rewritten; added mp.Pool.map to it
f7fea84
@sergpolly
allow symmetric diagsum to handle overlapping regions
3a89d28
@sergpolly
fix diagsum regions casting to ndarray
e6d9f09
@sergpolly
docstrings regarding regions2 touchedup in expected
f9ec065
@sergpolly
initial tests for newer expected
8a2a706
@sergpolly
minor test expected fixes, names and typos
2eb417c
@sergpolly
fixing requirements conflict: conda vs pip, travis please work
68931f9
@sergpolly
remove pytables fron conda-env in favor of tables in pip-reqs
b69befd
@sergpolly
drop conda-environment-yaml, update travis-config
fb4bfbe
@sergpolly
travis fix: source activate instead of conda activate
f54dc9b
@sergpolly
typo fix
125d1ea
@nvictus @sergpolly
Update .travis.yml
40c2c4b
@sergpolly
temporarily use bioframe-develop, make travis go
16686a1
@sergpolly
Merge remote-tracking branch 'max/expected_refactoring' into develop
c4a8180
@mimakaev
Restore bioframe>=0.1.0 requirement
6a90aef
@mimakaev
typo in bioframe requirement
f54b629
@mimakaev
Merge pull request #5 from dekkerlab/develop
f0ffacd 
minor diagsum fixes and expected test updates
@mimakaev
Merge branch 'expected_refactoring' into develop
8687c8a
@nvictus
Merge branch 'develop' of https://github.com/mirnylab/cooltools into …
b801272 
…develop
@nvictus
Update formatting
6cc2adf
@nvictus
Update formatting
4cd1e8b
@nvictus nvictus marked this pull request as ready for review September 9, 2020 01:23
@nvictus nvictus merged commit a0ee39d into master Sep 9, 2020
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6 participants

@mimakaev @nvictus @sergpolly @golobor @Phlya @itsameerkat