Comments (15)
Currently trying an upgrade.
from pybigwig.
Interesting, this is likely unrelated to the redirect but instead related to a certificate error in OSX. Did you install pyBigWig with bioconda or pip?
from pybigwig.
bioconda. I used the following:
conda install pybigwig -c bioconda
from pybigwig.
What's the output of conda list | grep curl
?
from pybigwig.
$ conda list | grep curl
curl 7.45.0 0
pycurl 7.19.5.3 py34_0
from pybigwig.
What happens if you conda install -c bioconda curl
(you might have to remove the one you currently have installed)? I made a version of curl for bioconda a year or so ago that fixed a few problems like this.
from pybigwig.
The upgrade seems to work! Thanks so much for your help.
Ran conda upgrade curl
. Now:
$ conda list | grep curl
curl 7.52.1 0
pycurl 7.43.0 py34_2
from pybigwig.
Cool, conda finally fixed their package! Glad that worked!
from pybigwig.
Hi! I came up with the same question even after I upgraded curl. How shall I solve this problem? Many thanks!
$ conda list | grep curl
curl 7.52.1 0 defaults
pycurl 7.43.0 py35_2 defaults
from pybigwig.
What version of OSX are both of you using? Maybe that's the difference? Perhaps I should add an option to libBigWig (what pyBigWig uses) to ignore certificate errors.
from pybigwig.
I download some bigwig files from ENCODE, and some of them works, but some are not. In addition, using url directly works well.
For example:
pyBigWig.open('https://www.encodeproject.org/files/ENCFF555VCB/@@download/ENCFF555VCB.bigWig')
works well.
pyBigWig.open('ENCFF555VCB.bigwig')
could not work after I download the file to my server.
The error message is:
[urlOpen] Couldn't open ENCFF555VCB.bigwig for reading
Sorry, this problem occurs in linux server.
from pybigwig.
Are you in the same directory as ENCFF555VCB.bigwig
?
from pybigwig.
Yes. In addition, I am wondering whether it is because the version of my installed pybigwig is too low. I installed it via bioconda, and the latest version of pybigwig is 0.2.8 in bioconda.
from pybigwig.
@kepbod: You'll get that error whenever there's an error opening a local file. This particular error will usually only happen if the file specified doesn't exist or you don't have rights to open it.
from pybigwig.
Oh, it is my fault. I figured out what is wrong that I used the wrong file name. Thanks for your assistance.
from pybigwig.
Related Issues (20)
- RuntimeError: Invalid interval bounds
- Document performance considerations? HOT 4
- Cannot add entries of value type int, but only float HOT 2
- support for osx-arm64 HOT 2
- numpy support broken in 0.3.18? HOT 1
- Create a BedGraph file using addEntries() throws segmentation fault HOT 2
- library import error HOT 4
- pyBigWig fails to find numpy installation when installing from PyPI HOT 5
- Writing a nan value should leave a gap HOT 7
- Can't enforce numpy features when pyBigWig is used as a dependency in downstream package HOT 5
- pip installation broken HOT 4
- Installing through pip not working HOT 9
- addHeader does not support multiple calls HOT 1
- Support for python >=3.11 HOT 1
- Issue Downloading pyBigWig HOT 1
- Simple patch to resolve conflict with roundup() macro
- Stats Sum Not Working as Expected
- 'zsh: segmentation fault ' HOT 1
- Out of memory listing entries on one human chromosome on a machine with 300 GB ram and 165 GB BigBed file HOT 1
- pyBigWig.entries() should return empty array, not None when no entries are found
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 pybigwig.