Hyphy Vision Not Working for ABSREL

[cahende]

Hello,

Hyphy Vision (the interactive online .json viewer) is not working for ABSREL output, please see sample output that produces the error (note I added the extension .txt to allow for attaching the file in github's messaging system but the file is still the .json output from ABSREL).

In addition, might I ask for a solution to extract relevant information from the .json from the command line for batch processing of output for large numbers of samples for this and MEME analysis (MEME works fine in hyPhy vision)?

Thank you, Cory Henderson Q7QJ32-absrel.json.txt

[spond]

Dear @cahende,

Regarding your aBSREL issue. Would it be possible to obtain the source data and the analysis settings which generated the .json? It contains some irregular branch records, and I am not entirely sure why.

As for batch json processing, you can go a variety of routes.

1. Use python's json module.
2. Use a command line utility jq to extract information from JSON (it's very powerful for this purpose)
3. Pretty much any modern language (R, Julia, Perl, Ruby) will support reading JSON files.

Best, Sergei

[cahende]

Thanks for the response Sergei!

The command I use for running hyPhy absrel is as follows (I run iteratively on a collection of MSA for some orthologs I have identified).

hyphy absrel --alignment MSA/alignedStopCodonRemoved/${field1}*.fa --tree iqTreeRuns/concord.cf.tree.nex --output hyphyRuns/ABSREL/${field1}-absrel.json

Attached is the MSA corresponding to the .json provided previously and my tree in nexus format.

Best,

Cory Henderson, Ph.D. Candidate NSF Graduate Research Fellow The Pennsylvania State University Rasgon Lab: Vector Genetics and Control https://rasgonlab.com/ Dept. of Molecular Cellular and Integrative Biosciences https://www.huck.psu.edu/content/research/center-for-infectious-disease-dynamics Center for Infectious Disease Dynamics https://www.huck.psu.edu/content/research/center-for-infectious-disease-dynamics

W-119 Millennium Science Complex Email: cah422@psu.edu Phone: (336)362-0549

On Wed, Feb 17, 2021 at 10:56 AM Sergei Pond notifications@github.com wrote:

Dear @cahende https://github.com/cahende,

Regarding your aBSREL issue. Would it be possible to obtain the source data and the analysis settings which generated the .json? It contains some irregular branch records, and I am not entirely sure why.

As for batch json processing, you can go a variety of routes.

1. Use python's json module.
2. Use a command line utility jq to extract information from JSON (it's very powerful for this purpose)
3. Pretty much any modern language (R, Julia, Perl, Ruby) will support reading JSON files.

Best, Sergei

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/veg/hyphy/issues/1286#issuecomment-780775227, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHBUWEXHKME4YRK6GZOGNLLS7QGMTANCNFSM4XYZDZ6A .

[spond]

Dear @cahende,

GitHub strips out e-mail attachments. Can you please re-attach here or send to me by e-mail directly?

Best, Sergei

[cahende]

Hi Sergei,

What email address would reach you directly?

Cory

On Feb 17, 2021, at 13:07, Sergei Pond notifications@github.com wrote:

 Dear @cahende,

GitHub strips out e-mail attachments. Can you please re-attach here or send to me by e-mail directly?

Best, Sergei

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[spond]

Dear @cahende,

spond at temple dot edu

Best, Sergei

[spond]

Resolved with da4ab4c3200a0db6f8d3a7f9b8cbd234fe5d47fe

As a workaround to view already existing ABSREL files, use https://observablehq.com/@spond/displaying-absrel-results-using-branch-censoring/2