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msettles / expHTS

Python application for "Experimental High Throughput Sequencing"
Apache License 2.0
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Contaminants confusion #50

Closed monicabritton closed 8 years ago

monicabritton commented 8 years ago

Synopsis: -A works but -c does not. (Matt fixed this in his local repo.)

Complete info: I created a folder, called contaminants. In the folder there is a symlink to a fasta file that I downloaded from NCBI (and have already used with bowtie2 and bwa). When I try to run this command:

expHTS preprocess -t 24 -w -c contaminants -f samples.txt -a

I get this error message: Traceback (most recent call last): File "/home/msettles/Python_venv/bin/expHTS", line 9, in load_entry_point('expHTS==1.0.1.dev2', 'console_scripts', 'expHTS')() File "/home/msettles/Python_venv/local/lib/python2.7/site-packages/expHTS-1.0.1.dev2-py2.7-linux-x86_64.egg/expHTS/init.py", line 18, in main expHTS.main() File "/home/msettles/Python_venv/local/lib/python2.7/site-packages/expHTS-1.0.1.dev2-py2.7-linux-x86_64.egg/expHTS/expHTS.py", line 167, in main commands[args.command].execute(args) File "/home/msettles/Python_venv/local/lib/python2.7/site-packages/expHTS-1.0.1.dev2-py2.7-linux-x86_64.egg/expHTS/preprocessCMD.py", line 108, in execute if os.path.exists(args.contaminatesFolder): AttributeError: 'Namespace' object has no attribute 'contaminatesFolder'

But the usage also shows -A as contaminants (or adapter contaminants). So I changed the command to -A and it ran, but I don't think that's correct

Also, it should be spelled "contaminants".

Thanks,

Monica

msettles commented 8 years ago

These were spelling errors in expHTS.py and preprocessCMD.py I’ve fixed the cause of the error and committed fixes to both master and develop

Matt

From: monicabritton notifications@github.com Reply-To: msettles/expHTS reply@reply.github.com Date: Friday, March 4, 2016 at 5:08 PM To: msettles/expHTS expHTS@noreply.github.com Subject: [expHTS] Contaminants confusion (#50)

Synopsis: -A works but -c does not. (Matt fixed this in his local repo.)

Complete info: I created a folder, called contaminants. In the folder there is a symlink to a fasta file that I downloaded from NCBI (and have already used with bowtie2 and bwa). When I try to run this command:

expHTS preprocess -t 24 -w -c contaminants -f samples.txt -a

I get this error message: Traceback (most recent call last): File "/home/msettles/Python_venv/bin/expHTS", line 9, in load_entry_point('expHTS==1.0.1.dev2', 'console_scripts', 'expHTS')() File "/home/msettles/Python_venv/local/lib/python2.7/site-packages/expHTS-1.0.1.dev2-py2.7-linux-x86_64.egg/expHTS/init.py", line 18, in main expHTS.main() File "/home/msettles/Python_venv/local/lib/python2.7/site-packages/expHTS-1.0.1.dev2-py2.7-linux-x86_64.egg/expHTS/expHTS.py", line 167, in main commands[args.command].execute(args) File "/home/msettles/Python_venv/local/lib/python2.7/site-packages/expHTS-1.0.1.dev2-py2.7-linux-x86_64.egg/expHTS/preprocessCMD.py", line 108, in execute if os.path.exists(args.contaminatesFolder): AttributeError: 'Namespace' object has no attribute 'contaminatesFolder'

But the usage also shows -A as contaminants (or adapter contaminants). So I changed the command to -A and it ran, but I don't think that's correct

Also, it should be spelled "contaminants".

Thanks,

Monica

— Reply to this email directly or view it on GitHub.

dstreett commented 8 years ago

Thanks, Matt! Just pulled the changes on the servers over here.

msettles commented 8 years ago

Ya! Collaborative development On Mar 8, 2016 11:12 AM, "David Streett" notifications@github.com wrote:

Thanks, Matt! Just pulled the changes on the servers over here.

— Reply to this email directly or view it on GitHub https://github.com/msettles/expHTS/issues/50#issuecomment-193922070.