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Questions and answers => General discussions (Q&As) => Topic started by: mauricio esguerra on September 02, 2009, 12:33:37 pm

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Title: Option not to display calculation status to screen.
Post by: mauricio esguerra on September 02, 2009, 12:33:37 pm

Hi Xiang-Jun,

I am running a script for rebuilding a large amount of random dsRNA conformations and then I run find_pair and analyze on the resulting pdb output.
Since I am generating a lot of data I would like to suppress the output to screen because I am sending this to a cluster which generates a bulky error log with the data that find_pair and analyze send to screen.
What I mean more precisely is that if I run find_pair, say:

Code: [Select]

bash# find_pair rna1.pdb stdout | analyze
I get some 3DNA information (output to screen) telling me how the calculation is doing, that is, something like:

Code: [Select]

...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: baselist.dat ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......

Time used: 00:00:00:01

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: baselist.dat ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: baselist.dat ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: raster3d.par ......

Time used: 00:00:00:02
Since I have already checked to see that my output files are right, I don't need this output. I am wondering if there is an internal command to suppress such output.

Thank you,

Mauricio

Title: Re: Option not to display calculation status to screen.
Post by: xiangjun on September 02, 2009, 11:28:37 pm

Hi Mauricio,

Thanks for formulating your question so clearly, especially for providing an example. Browsing the forum, one would find how many times I have asked for clarifications so I can understand what a question is about, exactly.

Okay, now back to your question.

Ideally, I could have provided a -q option (for quiet, or something similar) so the output message can be suppressed. As current is with 3DNA, however, the diagnostic information is directed to stderr. This should not be a problem in real life, with the help of Unix/Linux file redirection.

Again, an example would make the point clear. So let's use 'bdl084.pdb', you need to do the following:

Code: [Select]

find_pair bdl084.pdb bp_info 2> msg1
analyze bp_info 2> msg2

# or by combining them as this
find_pair bdl084.pdb stdout 2> msg1 | analyze 2> msg2
Note I am using bash shell. For other shells, you may need to use something different. Of course, you could also play with some variants along the line.

HTH,

Xiang-Jun

Title: Re: Option not to display calculation status to screen.
Post by: mauricio esguerra on September 03, 2009, 03:52:19 pm

Wow!
Thank you very much. That's great.
I should have checked in my Linux/Unix book about redirectioning first.

Thanks again,

Mauricio

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University