SVG generated in IGB 9.0.1 (OSX 10.13.6) works correctly in both Adobe Illustrator and Inkscape. CorelDRAW is only available on Windows so I was not able to test.

User could try using Inkscape in the meantime, unless the issue is on their end. HELP-92 had an issue where the user's computer was set to a language with non ASCII characters, leading to IGB outputting invalid SVG files.

The user provided SVG files (3.1C_tissues1.svg and 3C_tissues1.svg) both open correctly in Adobe Illustrator and Inkscape.

As the user stated that the files did not open in CorelDraw, it would be good to test on our systems. CorelDRAW is only available for Windows, so someone with a windows machine would need to test it (using the free trial download). Generate a SVG image in IGB 9.0.1 and see if it can be opened in CorelDraw.

Removing the text from the date field within the SVG solved the issue according to the user. This indicates the issue is related to HELP-92 where non-ASCII characters are being inserted into the date field, causing some programs (CorelDRAW) to consider the files corrupt. A work around for users is to manually remove the characters from the date field within the SVG file using a text editor.

I'm uncertain as to why Illustrator and Inkscape can open the problem SVG files and CorelDRAW cannot. CorelDRAW must be stricter in checking the SVG file.

User files added to Dropbox > IGB > Jira Issues > HELP-311

Ann Loraine <Ann.Loraine@uncc.edu> Tue, Nov 13, 2018 at 8:55 AM
To: miriam115@walla.co.il
Cc: "Freese, Nowlan" <nfreese@uncc.edu>, Mason Meyer <mmeyer20@uncc.edu>, Jill Jenkins <jjenki76@uncc.edu>
Hello,

Thank you for letting us know about this problem.

I'm forwarding your message to the IGB developers and support specialists.

It would be helpful if you could send us the files that are causing the problem for you. Hopefully we can diagnose the problem based on that.

Many thanks,

Ann

On Tue, Nov 13, 2018 at 8:37 AM, Support (JIRA) <lorainelabuncc@gmail.com> wrote:
Support created an issue

User Support / Bug HELP-311
Problem with exporting SVG from 9.0.1
Issue Type: Bug Bug
Assignee: Ann Loraine
Created: 13/Nov/18 1:36 PM
Labels: collector-b04cfbf9
Reporter: Support
Hello,
I use IGB on regular basis and I love it. Thank you!
I saved some SVG images last week and edited them in CorelDRAW X8, as I did many times before.
However, I just updated the version to 9.0.1, and now every time I try to open the new images I created, CorelDRAW X8 crashes. Since 'old' SVG open with no problem, and this crash happens in different computers, and the same thing exactly happens with CorelDRAW X6, I wondered if this may be a problem at your end.
I hope you can kindly reply ASAP, since I really need these images...
Thanks
Miriam

Reporter: Miriam
E-mail: miriam115@walla.co.il

–

Ann Loraine, Ph.D.
Dept. of Bioinformatics & Genomics
UNC Charlotte
704-687-0144 (office)
http://www.lorainelab.org
http://www.bitbucket.org/lorainelab
http://www.bioviz.org
https://svn.bioviz.org/viewvc/genomes/quickload

<miriam115@walla.co.il> Wed, Nov 14, 2018 at 4:50 AM
Reply-To: miriam115@walla.co.il
To: Ann.Loraine@uncc.edu, nfreese@uncc.edu, mmeyer20@uncc.edu, jjenki76@uncc.edu
Cc: "\"Freese, Nowlan\"" <nfreese@uncc.edu>, Mason Meyer <mmeyer20@uncc.edu>, Jill Jenkins <jjenki76@uncc.edu>
Dear Ann,
Thank you for your response.
Attached is two of the SVG files.
For my needs, I was able to convert the files online to different vector formats and edit them. But this of course is a temporary solution...
Thanks again
Miriam

Support created an issue

User Support / Bug HELP-311
Problem with exporting SVG from 9.0.1
Issue Type: Bug Bug
Assignee: Ann Loraine
Created: 13/Nov/18 1:36 PM
Labels: collector-b04cfbf9
Reporter: Support
[Quoted text hidden]
Reporter: Miriam
E-mail: miriam115@walla..co.il

–

Ann Loraine, Ph.D.
Dept. of Bioinformatics & Genomics
UNC Charlotte
704-687-0144 (office)
http://www.lorainelab.org
http://www.bitbucket.org/lorainelab
http://www.bioviz.org
https://svn.bioviz.org/viewvc/genomes/quickload

3.1C_tissues1.svg
1551K
3C_tissues1.svg
1340K

Nowlan Freese <nfreese@uncc.edu> Wed, Nov 14, 2018 at 8:59 AM
To: miriam115@walla.co.il
Cc: Ann Loraine <Ann.Loraine@uncc.edu>, Mason Meyer <mmeyer20@uncc.edu>, jjenki76@uncc.edu
Hi Miriam,

Could you please test the attached file and let me know if it works?

Nowlan

3.1C_tissues1_EDITED.svg
1543K

<miriam115@walla.co.il> Thu, Nov 15, 2018 at 6:50 AM
Reply-To: miriam115@walla.co.il
To: nfreese@uncc.edu, Ann.Loraine@uncc.edu, mmeyer20@uncc.edu, jjenki76@uncc.edu
Cc: Ann Loraine <Ann.Loraine@uncc.edu>, Mason Meyer <mmeyer20@uncc.edu>, "<jjenki76@uncc.edu>" <jjenki76@uncc.edu>
Hi Nowlen,

Yes, it worked perfectly!

Thanks
Miriam

User Support / Bug HELP-311
Problem with exporting SVG from 9.0.1
Issue Type: Bug Bug
Assignee: Ann Loraine
Created: 13/Nov/18 1:36 PM
Labels: collector-b04cfbf9
Reporter: Support
[Quoted text hidden]
I saved some SVG images last week and edited them in CorelDRAW X8, as I did many times before..
However, I just updated the version to 9.0.1, and now every time I try to open the new images I created, CorelDRAW X8 crashes. Since 'old' SVG open with no problem, and this crash happens in different computers, and the same thing exactly happens with CorelDRAW X6, I wondered if this may be a problem at your end.
I hope you can kindly reply ASAP, since I really need these images...
Thanks
Miriam
Reporter: Miriam
E-mail: miriam115@walla..co.il

–

Ann Loraine, Ph.D.
Dept. of Bioinformatics & Genomics
UNC Charlotte
704-687-0144 (office)
http://www.lorainelab.org
http://www.bitbucket.org/lorainelab
http://www.bioviz.org
https://svn.bioviz.org/viewvc/genomes/quickload

Nowlan Freese <nfreese@uncc.edu> Thu, Nov 15, 2018 at 9:01 AM
To: miriam115@walla.co.il
Cc: Ann Loraine <Ann.Loraine@uncc.edu>, Mason Meyer <mmeyer20@uncc.edu>, jjenki76@uncc.edu
Glad to hear it worked!

The only change I made was to remove the Date information on line 16 of the SVG file:
Original 3.1C_tissues1.svg:
<desc>Creator: Producer: org.freehep.graphicsio.svg.SVGGraphics2D Revision Source: Date: 15:00:48 IST ??? ????? 13 ?????? 2018</desc>

Edited 3.1C_tissues1.svg:
<desc>Creator: Producer: org.freehep.graphicsio.svg.SVGGraphics2D Revision Source: Date:</desc>

It appears that CorelDRAW is unhappy with the way the information in the Date field is formatted, and that removing it resolves the issue. We will investigate more on our end.

Best,

Nowlan

Re-assigning to developer who solved the issue.
You don't need to do anything further – this is for record-keeping/credit purposes only.
Thank you!

Hi,

I hope you can help me again. I'm trying to do the same thing: export from IGB to CorelDraw, but something weird is happening....
When I try importing an old SVG (exported from IGB), everything is working perfectly. Any other SVG is working fine too. However, any of the SVGs I exported recently are not opening properly in CorelDraw (in Chrome they look fine). In the best case scenario, two very long horizontal lines appear. If I do CTRL+U twice, and delete these lines, I'm able to locate a small mirror image of the tracks I was trying to export. I tried this in a few IGB versions, same results. Converting the files to a different format didn't solve the problem. I also have edited the date to remove the question marks.
Any ideas what I can do?
I attached two files - the new one was exported from version 9.1.4, the old one is from 9.0.2.

Thank you

Miriam

Hi Miriam,

I compared the two files and I can't find anything wrong with the new file. I can load both files in Inkscape (I still don't have access to CorelDraw). I also don't think we have made any changes recently to how svg files are created in IGB.

I've attached two files that I would like you to try to load into CorelDraw and tell me if they appear correctly. I took the new igb file you provided, opened it in inkscape, and then saved it through inkscape as an svg. When I compared it to the original file it appears inkscape has updated/changed the svg formatting. The other file was also created from the new igb file you provided. I have removed two long horizontal lines using inkscape and then saved the file as an svg using inkscape.

Let me know if either of these files works for you in CorelDraw, as it may give me some clues as to what the problem may be.

Best,

Nowlan

Hi Nowlan,

Thanks for your prompt answer.

Both of the original files didn't work properly, from both IGB versions. I am attaching now a file which works fine from March (note that it has the question marks in the date stamp, but it still works fine). An additional file I tried (exported during June) didn't work - had the same horizontal line issue.

I tried out the two files you sent - the one with the horizontal lines did the same thing as my original files, and the one without the lines worked as expected (both look fine when opening them Chrome).

I found out that also in my files I can delete the horizontal lines - to do that I decrease the size to 1% of the original, delete the lines, and then increase by 50,000% to get a full A4 image (the mirroring of the image was caused at this step, and not from the file itself). This is a solution, but it requires some effort just to start the editing of the picture... I also noted that the importing takes CorelDraw much more time than usual.

.

Thank you

Miriam

Hi Miriam,

Just to confirm, the file chr5_w_high__new_igb_EDITED.svg opened correctly in CorelDraw?

Regarding the IGB Quickload not appearing, can you take a screenshot of the Data Sources menu for me? To get there, click the Configure button in the Available Data box. It looks like the IGB Quickload might not be reachable for some reason.

I will keep looking into the svg issue.

Best,

Nowlan

Hi Nowlen,

Yes, it does. Please see the attached screenshot from CorelDraw, as it looks after importing.
I am also attaching the data sources from the new & old versions (the one on the left is the new one).

Thanks again
Miriam

The Araport annotations should still be available through IGB Quickload. It looks like IGB Quickload is available in your screenshots, so I'm not sure why Araport wouldn't show up.

Try refreshing the Quickload connection by clicking Screen Shot 2020-11-18 at 4.04.26 PM.png in the Data Sources menu and then sending me whatever information appears in the IGB console (Help > Show Console). If that doesn't work then you can try resetting preferences to default. This will restart IGB and reset all of the IGB settings to their defaults. Click IntegratedGenomeBrowser > Preferences > Other Options > Reset Preference to Defaults

Hi Miriam,

The problem with the svg seems to be related to IGB including a very long bar in the svg file. For example,in the chr5_w_high__new_igb.svg file, lines 25 and 33,043 specify a thin line from -362347.5 to 622531.5.

I can replicate the issue in IGB by going to Arabidopsis chr1:8,688,527-8,689,303 and loading the graph from the quickload data RNA-Seq > SM > Graph > Pollen, coverage. When I export the image as svg Main View the svg image includes the long lines. This seems to be an issue with IGB drawing the lines in graph tracks that span the entire chromosome. If I remove the graph track from IGB and resave the svg the lines no longer appear. I also tried older versions of IGB back to 8.0.0 and the lines are still present in the graph track, so it does not seem to be related to the version of IGB, but rather the type of data that has been loaded.

I will need to take a closer look at why this is happening and if there is a way for us to remove the lines in the future. It seems like manually deleting the lines from the svg may be the only option for now.

Best,

Nowlan

Hi Nowlen,

Thank you - resetting the preferences solved the missing annotations problem.

The data I am trying to export now is in bigwig format (.bw). I tried exporting now bedgraph format (.bedgraph), and it worked fine (attached).

Based on what you wrote, I deleted some rows from the svg file - I searched for 808080, and deleted tha row and the next 2 (a total of three rows). It now looked almost normal in CorelDraw - the right half of the image is white (no data was lost, it's just a white expansion) which appears in the 'try' svg as well.

I will carry on doing this for now. Thank you very much for your time and efforts!

Best,

Miriam