Comments (9)
Thanks for the information, I'll fix this when I get at work, in a few hours.
from fastqmetrics.
I'll consider this solved - please let me know if you experience further issues.
from fastqmetrics.
Thanks for reporting!
Oops, that was a little oversight. I changed the name of the function after pushing to pypi, apparently. Stupid. I just pushed nanoget 0.14.1 to pypi which should contain the correct function name stream_fastq_full
. Updating using pip install nanoget --upgrade
should do the trick...
from fastqmetrics.
Thank you. But now we have a new one,
readname length averageQ medianQ
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/usr/local/lib/python3.6/site-packages/nanoget/nanoget.py", line 330, in extract_all_from_fastq
nanomath.median_qual(rec.letter_annotations["phred_quality"]))
AttributeError: module 'nanomath' has no attribute 'median_qual'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/bin/fastqmetrics", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python3.6/site-packages/fastqmetrics/fastqmetrics.py", line 9, in main
for res in stream_fastq_full(args.fastq, args.threads):
File "/usr/local/lib/python3.6/site-packages/nanoget/nanoget.py", line 304, in stream_fastq_full
for results in pool.imap(extract_all_from_fastq, SeqIO.parse(inputfastq, "fastq")):
File "/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/pool.py", line 735, in next
raise value
AttributeError: module 'nanomath' has no attribute 'median_qual'
from fastqmetrics.
Is nanomath the latest version? Updating could fix this. I have been a bit sloppy with specifying the required version it seems. Apologies!
from fastqmetrics.
Yes nanomath is the latest version.
pip3 install nanomath --upgrade
Requirement already up-to-date: nanomath in /usr/local/lib/python3.6/site-packages
Requirement already up-to-date: pandas in /usr/local/lib/python3.6/site-packages (from nanomath)
Requirement already up-to-date: numpy>1.8 in /usr/local/lib/python3.6/site-packages (from nanomath)
Requirement already up-to-date: pytz>=2011k in /usr/local/lib/python3.6/site-packages (from pandas->nanomath)
Requirement already up-to-date: python-dateutil>=2 in /usr/local/lib/python3.6/site-packages (from pandas->nanomath)
Requirement already up-to-date: six>=1.5 in /usr/local/lib/python3.6/site-packages (from python-dateutil>=2->pandas->nanomath)
from fastqmetrics.
Can you please tell me the version number too?
python - c "import nanomath ; print(nanomath.__version__)"
from fastqmetrics.
This what I have;
python3 -c "import nanomath; print(nanomath.__version__)"
0.13.0
from fastqmetrics.
I think this should be fixed with nanomath 0.13.1
from fastqmetrics.
Related Issues (1)
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 fastqmetrics.