Comments (7)
baudrly
commented on June 12, 2024
Hello,
in line 667 of network.py, could you try replacing the following:
parser.add_argument('-i', '--input', type=argparse.FileType('r'),
with:
parser.add_argument('-i', '--input',
and report back if the error still shows up?
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cpadillla1331
commented on June 12, 2024
Thanks! Now I’m getting a different error…
File “/home_dir/metaTOR-master/network.py", line 749, in <module>
parameters=parameters)
File "/home_dir/metaTOR-master/network.py", line 157, in alignment_to_contacts
contig_name_forward = read_forward.reference_name
AttributeError: 'pysam.calignmentfile.AlignedSegment' object has no attribute 'reference_name'
From: baudrly <[email protected]>
Reply-To: koszullab/metaTOR <[email protected]>
Date: Wednesday, June 6, 2018 at 12:05 AM
To: koszullab/metaTOR <[email protected]>
Cc: Cory Padilla <[email protected]>, Author <[email protected]>
Subject: Re: [koszullab/metaTOR] network.py TypeError: Argument must be string or unicode. (#3)
parser.add_argument('-i', '--input'
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baudrly
commented on June 12, 2024
What version of pysam are you using? If not the latest, could you try upgrading it and see if the error still persists?
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cpadillla1331
commented on June 12, 2024
It looks like I’m using the latest pysam 0.14.1.
From: baudrly <[email protected]>
Reply-To: koszullab/metaTOR <[email protected]>
Date: Wednesday, June 6, 2018 at 12:02 PM
To: koszullab/metaTOR <[email protected]>
Cc: Cory Padilla <[email protected]>, Author <[email protected]>
Subject: Re: [koszullab/metaTOR] network.py TypeError: Argument must be string or unicode. (#3)
What version of pysam are you using? If not the latest, could you try upgrading it and see if the error still persists?
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baudrly
commented on June 12, 2024
I'm having trouble reproducing your error. Apparently it shows up in earlier versions of pysam but should not occur if you're using the latest version. Maybe it's a python2 vs. 3 issue? What's the output of pip show pysam vs. pip3 show pysam?
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cpadillla1331
commented on June 12, 2024
They look the same… I found out I don’t have sudo privileges on this machine. I set myself on an AWS instance and got it working like a charm! I’m not exactly sure why that made the difference, but it’s working great. Also just a heads up the link download the moduleHMMs is no longer a valid link.
$ pip show pysam
…---
Metadata-Version: 2.0
Name: pysam
Version: 0.14
Summary: pysam
Home-page: https://github.com/pysam-developers/pysam
Author: Andreas Heger
Author-email: [email protected]
Installer: pip
License: MIT
Location: /usr/local/lib/python3.4/dist-packages
Requires:
Classifiers:
Development Status :: 4 - Beta
Intended Audience :: Science/Research
Intended Audience :: Developers
License :: OSI Approved
Programming Language :: Python
Topic :: Software Development
Topic :: Scientific/Engineering
Operating System :: POSIX
Operating System :: Unix
Operating System :: MacOS
$ pip3 show pysam
---
Metadata-Version: 2.0
Name: pysam
Version: 0.14
Summary: pysam
Home-page: https://github.com/pysam-developers/pysam
Author: Andreas Heger
Author-email: [email protected]
Installer: pip
License: MIT
Location: /usr/local/lib/python3.4/dist-packages
Requires:
Classifiers:
Development Status :: 4 - Beta
Intended Audience :: Science/Research
Intended Audience :: Developers
License :: OSI Approved
Programming Language :: Python
Topic :: Software Development
Topic :: Scientific/Engineering
Operating System :: POSIX
Operating System :: Unix
Operating System :: MacOS
From: baudrly <[email protected]>
Reply-To: koszullab/metaTOR <[email protected]>
Date: Wednesday, June 20, 2018 at 1:01 AM
To: koszullab/metaTOR <[email protected]>
Cc: Cory Padilla <[email protected]>, Author <[email protected]>
Subject: Re: [koszullab/metaTOR] network.py TypeError: Argument must be string or unicode. (#3)
I'm having trouble reproducing your error. Apparently it shows up in earlier versions of pysam<CGATOxford/UMI-tools#199> but should not occur if you're using the latest version. Maybe it's a python2 vs. 3 issue? What's the output of pip show pysam vs. pip3 show pysam?
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You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#3 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AhTek0nUpmEfq78PjqxZjafcrBkyt2w2ks5t-gFMgaJpZM4UbNs_>.
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baudrly
commented on June 12, 2024
Thanks for the heads up! I fixed the link.
As for the pysam-related error, it is maybe due to the python instance being called by the script not being the same as the one with the updated version of pysam. Not sure how it could happen though.
Edit: Since the error seems to be environment-related, I'm closing this until someone else reports it as well.
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Related Issues (11)
- VisibleDeprecationWarning when running "bins.py" HOT 4
- HMM database HOT 3
- Recursive Louvain Binning HOT 1
- KeyError: 'LOUVAIN_PATH' HOT 1
- Allocation of external dependencies & extra suggestions HOT 1
- ValueError: too many values to unpack HOT 11
- Link to annotation database is broken HOT 2
- Failure to produce bin fasta files HOT 4
- .hmm file existence in the HMM_databases folder HOT 2
- Link to MetaTOR manual in Tutorial gives 404 HOT 1
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