Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Author Topic: dssr stdin  (Read 4673 times)

Offline zcx

  • non-commercial
  • with-posts
  • *
  • Posts: 4
    • View Profile
dssr stdin
« 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.

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1640
    • View Profile
    • 3DNA homepage
Re: dssr stdin
« Reply #1 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

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1640
    • View Profile
    • 3DNA homepage
Re: dssr stdin
« Reply #2 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
« Last Edit: May 31, 2020, 11:55:00 am by xiangjun »

Offline zcx

  • non-commercial
  • with-posts
  • *
  • Posts: 4
    • View Profile
Re: dssr stdin
« Reply #3 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] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.