'IntervalTree' object has no attribute 'merge_neighbors'
Opened this issue · 11 comments
I am attempting to call merge_neighbors() on an IntervalTree instance, but I am running into the following error:
% ../test.py
IntervalTree([Interval(50, 80, {'chrom': 'chr1', 'id': 'F'}), Interval(100, 120, {'chrom': 'chr1', 'id': 'D'}), Interval(100, 140, {'chrom': 'chr1', 'id': 'C'}), Interval(120, 200, {'chrom': 'chr1', 'id': 'A'}), Interval(199, 260, {'chrom': 'chr1', 'id': 'B'})])
None
Traceback (most recent call last):
...
File "../test.py", line 44, in main
mn_tree = tree.copy().merge_neighbors()
AttributeError: 'IntervalTree' object has no attribute 'merge_neighbors'
Here is the minimal reproducible example script test.py:
#!/usr/bin/env python
import sys
import io
import intervaltree
test_intervals_str = '''chr1 50 80 F
chr1 100 120 D
chr1 100 140 C
chr1 120 200 A
chr1 199 260 B
'''
def main():
# build tree
tree = intervaltree.IntervalTree()
intervals = io.StringIO(test_intervals_str)
for interval in intervals:
(chrom, start, stop, id) = interval.rstrip().split('\t')
tree[int(start):int(stop)] = { 'chrom' : chrom, 'id' : id }
print(tree)
mo_tree = tree.copy().merge_overlaps()
print(mo_tree)
mn_tree = tree.copy().merge_neighbors()
print(mn_tree)
if __name__ == '__main__':
main()
It looks like merged_neighbors is in the version I am using (v3.1.0):
intervaltree/intervaltree/intervaltree.py
Lines 770 to 776 in 328d6db
Here is my install log:
% git clone https://github.com/chaimleib/intervaltree.git
% cd intervaltree
% python ./setup.py install
!!!>>> This is a RELEASE version <<<!!!
Version: 3.1.0
running install
running bdist_egg
running egg_info
writing intervaltree.egg-info/PKG-INFO
writing dependency_links to intervaltree.egg-info/dependency_links.txt
writing requirements to intervaltree.egg-info/requires.txt
writing top-level names to intervaltree.egg-info/top_level.txt
reading manifest file 'intervaltree.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'intervaltree.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.9-x86_64/egg
running install_lib
running build_py
creating build/bdist.macosx-10.9-x86_64/egg
creating build/bdist.macosx-10.9-x86_64/egg/intervaltree
copying build/lib/intervaltree/intervaltree.py -> build/bdist.macosx-10.9-x86_64/egg/intervaltree
copying build/lib/intervaltree/interval.py -> build/bdist.macosx-10.9-x86_64/egg/intervaltree
copying build/lib/intervaltree/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/intervaltree
copying build/lib/intervaltree/node.py -> build/bdist.macosx-10.9-x86_64/egg/intervaltree
byte-compiling build/bdist.macosx-10.9-x86_64/egg/intervaltree/intervaltree.py to intervaltree.cpython-38.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/intervaltree/interval.py to interval.cpython-38.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/intervaltree/__init__.py to __init__.cpython-38.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/intervaltree/node.py to node.cpython-38.pyc
creating build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying intervaltree.egg-info/PKG-INFO -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying intervaltree.egg-info/SOURCES.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying intervaltree.egg-info/dependency_links.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying intervaltree.egg-info/requires.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying intervaltree.egg-info/top_level.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying intervaltree.egg-info/zip-safe -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
creating 'dist/intervaltree-3.1.0-py3.8.egg' and adding 'build/bdist.macosx-10.9-x86_64/egg' to it
removing 'build/bdist.macosx-10.9-x86_64/egg' (and everything under it)
Processing intervaltree-3.1.0-py3.8.egg
Removing /Users/areynolds/miniconda3/lib/python3.8/site-packages/intervaltree-3.1.0-py3.8.egg
Copying intervaltree-3.1.0-py3.8.egg to /Users/areynolds/miniconda3/lib/python3.8/site-packages
intervaltree 3.1.0 is already the active version in easy-install.pth
Installed /Users/areynolds/miniconda3/lib/python3.8/site-packages/intervaltree-3.1.0-py3.8.egg
Processing dependencies for intervaltree==3.1.0
Searching for sortedcontainers==2.4.0
Best match: sortedcontainers 2.4.0
Adding sortedcontainers 2.4.0 to easy-install.pth file
Using /Users/areynolds/miniconda3/lib/python3.8/site-packages
Finished processing dependencies for intervaltree==3.1.0
Am I not using merge_neighbors correctly, or is there some other issue? Thanks!
You have probably installed it wrong and used the released version rather than the current git master.
Note that the currently released version does not include the merge_neighbors feature.
See install log.
See install log.
It's still possible that you run the script in a wrong environment and use an older package which is installed elsewhere.
When running your script with intervaltree from git, it does not crash:
$ python3 test.py
IntervalTree([Interval(50, 80, {'chrom': 'chr1', 'id': 'F'}), Interval(100, 120, {'chrom': 'chr1', 'id': 'D'}), Interval(100, 140, {'chrom': 'chr1', 'id': 'C'}), Interval(120, 200, {'chrom': 'chr1', 'id': 'A'}), Interval(199, 260, {'chrom': 'chr1', 'id': 'B'})])
None
None
I don't think this is a bug in intervaltree.
The install log shows that this is installed via the git distribution. I am installing into a clean virtual environment.
The second output in your test run is not what I expect for overlapping intervals, but this is getting a bit afield from my question, in any case.
The second output in your test run is not what I expect for overlapping intervals, but this is getting a bit afield from my question, in any case.
merge_neighbors() does not return anything, it modifies the original tree, that's why it returns None.
Could we get a new release that includes merge_neighbors?
Are there any plans to release a new version that includes merge_neighbors?
great library! Very much need merge_neighbors method.. Any chance to make it working?
> It looks like merged_neighbors is in the version I am using (v3.1.0):
@alexpreynolds: I believe merge_neighbors(...) was added in my pull request, #105. @chaimleib has not yet pushed the latest code to PyPI.
You could install from GitHub in the meanwhile.
Edit: Oops, I misread this thread.
I would benefit from merge_neighbors being released as well