Details
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Type:
New Feature
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Labels:None
Description
From: Steve Chervitz <schervitz@personalis.com>
Date: Friday, February 20, 2015 at 9:41 PM
To: "Loraine, Ann" <Ann.Loraine@uncc.edu>, Loraine Lab <nfreese@uncc.edu>
Subject: Re: letter of support for IGB - Feb 23
Hi Ann & Nowlan,
Just letting you know that I should have my letter of support ready for you on Mon (2/23). I'm running it by my supervisors for approval now.
Btw, I have some questions for you regarding the script interface to IGB:
https://wiki.transvar.org/display/igbman/Scripting+and+the+IGB+command+language
What I'd like to be able to do programmatically is to:
- load multiple BAM files for a given chromosome;
- zoom to a particular region and load data for that region for all BAM tracks;
- create read depth graphs for each BAM file track;
- ensure the graphs are using the same Y-axis range; (for comparability across tracks)
- set the foreground color for a specific track (nice to have!);
- turn off display of the BAM file tracks (to show only the depth graphs + gene annotation track);
- generate an image file of the main display.
Can you let me know if this sort of control is possible using IGB's command language? It would be quite useful!
Thanks,
Steve
Attachments
Issue Links
- relates to
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IGBF-437 Add/Expand Additional IGB Scripting
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- To-Do
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Activity
| Workflow | classic default workflow [ 15698 ] | Loraine Lab Workflow [ 16414 ] |
| Resolution | Done [ 10000 ] | |
| Status | Open [ 1 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 16414 ] | Fall 2019 Workflow Update [ 20556 ] |
| Workflow | Fall 2019 Workflow Update [ 20556 ] | Revised Fall 2019 Workflow Update [ 22761 ] |
From: Nowlan Freese <nfreese@uncc.edu>
Date: February 25, 2015 at 6:43 AM
To:Steve Chervitz <schervitz@personalis.com> "Loraine, Ann" <Ann.Loraine@uncc.edu>,
Subject: Re: letter of support for IGB - Feb 23
Hi Dr. Chervitz,
I talked with David, our senior software developer, and unfortunately we don't have commands to create a depth graph, put the graphs on the same Y-axis, or to change the foreground color. Everything else we can do, please see the attached file for an example. There's a general agreement that these commands, and many others, need to be added in. I'll let you know once we have expanded the list of available commands, and if you have any suggestions for additional commands you would like to see then please let me know and I will add them to our list. Thanks!
Nowlan
Here's a list of all the currently available commands -
genome
goto
loadAllows multiple files to be specified, split by commas
loadfromserver
loadmode
print
refresh
selectAllows multiple gene ids to be specified, split by commas
selectfeature
sleep
sidetrackAllows multiple files to be specified, split by commas
showtrackAllows multiple files to be specified, split by commas
snapshot
snapshotwholeFrame
snapshotmainView
snapshotmainViewWithLabels
snapshotslicedViewWithLabels
homescreen
bringToFront