Comments (5)
still thinking about this. But once you have str(self), you can just test for equality, no need to hash.
So you could just have
def __hash__(self):
return str(self)
in which case, all you really need is to test if str(self) == str(other) in __richcmp__
all that said, i kinda like the idea of 2 intervals being equal
if their starts and stops are the same.
from pybedtools.
good points. str(self) == str(other) is easy to do if you want it, but testing chrom/start/stop is more annoying, and therefore better encapsulated in __richcmp__
.
two somewhat trickier questions though: 1) should strand continue to be ignored, and 2) should > and < have any meaning?
from pybedtools.
-
seems intuitive that strand should be taken into account.
-
maybe:
<
: strictly to the left of (not touching)
>
: strictly to the right of (not touching)
<=
: not>
>=
: not<
from pybedtools.
sounds good. i guess as long as it's well documented, there shouldn't be any surprises.
from pybedtools.
This has been implemented for a while now, using "profiles" of feature1/feature2 start/stop comparisons -- see
http://packages.python.org/pybedtools/topical-comparisons.html
Strand still isn't considered . . . just haven't needed it yet. Also, the semantics are currently different than what you suggest because I wasn't thinking about your comment when I was writing the code. That is, slightly overlapping features are both <=
as well as <
. But with the "profiles" this should be easy to change if needed -- see
pybedtools/pybedtools/cbedtools.pyx
Line 25 in b494b6b
from pybedtools.
Related Issues (20)
- Support Python 3.10 and 3.11 HOT 1
- "python setup.py bdist_wheel did not run successfully" when pip installing with python v3.11 HOT 8
- to_dataframe() creates 0th row with generic names in nucleotide_content HOT 2
- build failure under python 3.11 HOT 6
- pybedtools intersect error HOT 2
- Cannot create a BedTool object from list of regions that uses np.int64 coordinates
- remove historical py27 support HOT 1
- bedtools intersect reported incorrect interval intersection HOT 3
- Cythonizing files requires `language_level=2` to be set in cythonize() HOT 4
- pybedtools multi_bam_coverage assistance HOT 2
- "fastaFromBed" error HOT 2
- intersect with multiple -b arguments not working with -sorted HOT 1
- Unable to install pybedtools==0.9.1 in Python3.10 HOT 4
- Len modifying the Bedtools after a filter HOT 2
- Has pybedtools considered packaging bedtools? HOT 3
- how to mask gap regions for randomization? HOT 1
- Issue while doing pip install pybedtools HOT 3
- Inconsistent behaviour when using files from `pathlib.PosixPath` with BedTool functions...
- pybedtools.bedtool.Bedtool.sort()
- total_coverage giving a incorrect value
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pybedtools.