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Questions and answers => RNA structures (DSSR) => Topic started by: zcx on May 30, 2020, 11:45:49 am

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Title: dssr stdin
Post by: zcx on May 30, 2020, 11:45:49 am
Can x3dna-dssr uses stdin for input? The following flags apparent do not work (yet):
cat file.pdb | x3dna-dssr -i=stdin
cat file.pdb | x3dna-dssr -i=-
If there is source code for dssr, I am happy to help with implementing such a feature.
Title: Re: dssr stdin
Post by: xiangjun on May 30, 2020, 11:56:43 am
Quote
Can x3dna-dssr uses stdin for input?
Yes.

Quote
The following flags apparent do not work (yet):
cat file.pdb | x3dna-dssr -i=stdin
cat file.pdb | x3dna-dssr -i=-

When piping input to DSSR, users must specify the file format via --format. Assuming file.pdb is in PDB format, the following should work:

Code: [Select]
cat file.pdb | x3dna-dssr -i=stdin --format=pdb
cat file.pdb | x3dna-dssr -i=- --format=pdb

Please have a try and report back how it goes.

Best regards,

Xiang-Jun
Title: Re: dssr stdin
Post by: xiangjun on May 31, 2020, 11:37:20 am
Quote
If there is source code for dssr, I am happy to help with implementing such a feature.

Regarding the availability of DSSR source code, please see the thread "Source distribution/Linux packaging" (http://forum.x3dna.org/rna-structures/source-distributionlinux-packaging/). DSSR 2.0 (to be released) will be formally licensed by Columbia University.

There are open source alternatives to DSSR, including MC-Annotate, RNAView, and FR3D, that may better suit your needs.

BTW, does the suggested method work? As a general principle, the user who starts a thread is expected to provide a summary, or at least a simple yes/no response. Other viewers of the thread will benefit from your effort. It will also give me more incentive to answer your future DSSR-related questions (if any).

Best regards,

Xiang-Jun
Title: Re: dssr stdin
Post by: zcx on June 08, 2020, 03:51:39 pm
Yes, stdin works, thank you. It will be good if this feature is documented in the program.

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.