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daler
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pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
http://daler.github.io/pybedtools
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Handling of wide pseudo-bed files (pseudo-bed files interpreted as .sam)?
#363
semenko
closed
2 years ago
2
numpy.int64 has no attribute isdigit
#362
urrik98
closed
2 years ago
4
NotImplementedError: "intersectBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method.
#361
stanleyjs
closed
2 years ago
7
Move to MIT license, v0.9 (fix #286)
#360
daler
closed
2 years ago
0
Fix 355
#359
daler
closed
2 years ago
0
Fix 348
#358
daler
closed
2 years ago
0
fix #345 (and a better fix for #81 too)
#357
daler
closed
2 years ago
0
fix #343
#356
daler
closed
2 years ago
0
POS-field in VCF files and intervals derived from them
#355
DRL
closed
2 years ago
1
BEDtools can handle more than 510 files at a time
#354
leeleavitt
closed
1 year ago
1
docs: Fix a few typos
#353
timgates42
closed
2 years ago
0
Loss of tag-value pairs in GFF attribute field with duplicated tags after accessing interval.attrs
#352
ijhoskins
closed
2 years ago
4
Remove remnants of Python 2.7 support
#351
DavidCain
closed
2 years ago
2
Update package classifiers stating Python support
#350
DavidCain
closed
2 years ago
3
Make the build reproducible
#349
lamby
closed
3 years ago
1
Issue with the initialization of otherfileds in Interval
#348
Shrulik
closed
2 years ago
0
NotImplementedError: "intersectBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method
#347
starboyvarun
closed
3 years ago
0
module 'pybedtools' has no attribute 'featurefuncs'
#346
quantumdot
closed
2 years ago
1
unexpected behavior due to bedtools bug, might better considering put the "-a" options to ahead in _cmds
#345
xubeisi
closed
2 years ago
0
Error When Running Shuffle
#344
Jome0169
closed
3 years ago
1
remove_invalid not removing entries with start and stop negative
#343
blaiseli
closed
2 years ago
6
Test suite fails with 1 value error and 8 assertion errors.
#342
TheChymera
closed
2 years ago
6
only push docs on py38
#341
daler
closed
3 years ago
0
python3.8 - runtime warning
#340
roni-fultheim
closed
3 years ago
5
GitHub actions
#339
daler
closed
3 years ago
0
V0.8.2
#338
daler
closed
3 years ago
0
Temporary files usage
#337
ngualand
closed
3 years ago
1
Errors being thrown after python (3.9.1), pybedtools updates
#336
mcnaircm
closed
2 years ago
2
intersect threshold
#335
berkuva
closed
3 years ago
1
Fix pandas empty file err when bedtools output is empty https://github.com/daler/pybedtools/issues/333#issue-806822728
#334
gopi1616
closed
3 years ago
0
Pandas throws EmptyDataError when bedtools results are empty [bedtool.py, in to_dataframe() line 3688]
#333
gopi1616
closed
3 years ago
1
Intersecting two pandas DataFrames
#332
KaparaNewbie
opened
3 years ago
0
Pypi version discrepancies.
#331
DriesSchaumont
closed
3 years ago
2
Is it possible to keep column information after intersecting?
#330
PanZiwei
closed
3 years ago
0
0.8.0 tests fail with `No module named 'pybedtools.cbedtools'`
#329
TheChymera
closed
3 years ago
1
Failed to build pybedtools (pip install pybedtools)
#328
kiranchari
closed
4 years ago
1
Merge is not working as expected
#327
emilyleventhal
closed
4 years ago
0
Ignore bedtools warnings that are not capitalized
#326
JureZmrzlikar
closed
3 years ago
0
Intervals when using UCSC genome are wrong (pybedtools is 0-based and doesn't correct for 1-based?)
#325
gwangjinkim
closed
3 years ago
1
run tests on Python 3.8
#324
daler
closed
4 years ago
0
proof of concept genomepy integration
#323
simonvh
closed
4 years ago
5
RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode
#322
mgalardini
closed
4 years ago
3
from_dataframe only extracting first character of feature start and end position
#321
jbhiatt
closed
4 years ago
2
closes #319
#320
naumenko-sa
closed
4 years ago
6
error reading unicode symbols in the vcf.gz file
#319
naumenko-sa
closed
4 years ago
1
Auto-cythonize when .ccp are missing.
#318
blaiseli
closed
3 years ago
0
Automatically try to run cythonize when needed while installing from source
#317
blaiseli
closed
3 years ago
6
import error on bedtools from pybedtools
#316
rthapa26
closed
4 years ago
4
Ideas for the next major release
#315
daler
opened
4 years ago
0
update random_subset to use optional fractions
#314
daler
closed
4 years ago
0
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