Giter VIP home page Giter VIP logo

Comments (9)

wdecoster avatar wdecoster commented on July 17, 2024 1

Thanks for the information, I'll fix this when I get at work, in a few hours.

from fastqmetrics.

wdecoster avatar wdecoster commented on July 17, 2024 1

I'll consider this solved - please let me know if you experience further issues.

from fastqmetrics.

wdecoster avatar wdecoster commented on July 17, 2024

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.

george-githinji avatar george-githinji commented on July 17, 2024

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.

wdecoster avatar wdecoster commented on July 17, 2024

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.

george-githinji avatar george-githinji commented on July 17, 2024

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.

wdecoster avatar wdecoster commented on July 17, 2024

Can you please tell me the version number too?
python - c "import nanomath ; print(nanomath.__version__)"

from fastqmetrics.

george-githinji avatar george-githinji commented on July 17, 2024

This what I have;

python3 -c "import nanomath; print(nanomath.__version__)"
0.13.0

from fastqmetrics.

wdecoster avatar wdecoster commented on July 17, 2024

I think this should be fixed with nanomath 0.13.1

from fastqmetrics.

Related Issues (1)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo 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.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.