Please provide download of results from website

[mmokrejs]

Hi, I lack an option to download my results from http://qb.cshl.edu/genomescope website. I also tried from firex "Save as" and wget --mirror -l2 but they both failed.

Ideally if one could group results and get animated GIF figures (I ran k-mer counting at various k-mer sizes).

Thank you

[mschatz]

Can you give the full URL you are trying? You should be able to save the plots by using the "Save As" menu option in your browser. For example, here is the full URL for a recent run: http://qb.cshl.edu/genomescope/analysis.php?code=UyWTAXyzTJK6mHZPnqxh

And the individual plots can be accessed like this: http://qb.cshl.edu/genomescope/user_data/UyWTAXyzTJK6mHZPnqxh/plot.png http://qb.cshl.edu/genomescope/user_data/UyWTAXyzTJK6mHZPnqxh/plot.log.png

I would not use wget since the computation runs on the fly and can take 30 seconds to 1 minute to compute so wget might time out.

Hope this helps

Mike

[mmokrejs]

I was downloading a URL like the http://qb.cshl.edu/genomescope/analysis.php?code=UyWTAXyzTJK6mHZPnqxh . Would there be a hyperlink from the page to plot.png and plot.log.png I could have fetched just that too.

Yeah, I went better to fetch the 474MB of genomescope.git and ran the command locally. I haven't realized before you always re-create the results page on the fly. Hmm, that complicates the situation admittedly.

An animated GIF could have been created using convert (part of ImageMagick):

figures=`find . -name plot.png | sort | while read f; do echo -n "$f "; done`
figure_series=`for a in $figures; do printf -- "-delay 1000 %s " $a; done`
convert $figure_series animation.gif

The sort step could be improved to do natural type of sorting, but you get the point.

[mschatz]

As it is now, we expect users to work interactively in the browser so they can just download the plots there. If you want to run it on the command line, it is really just one script that you need (the repo has the testing data so we can do regression tests): https://github.com/schatzlab/genomescope/blob/master/genomescope.R

The current interface doesnt support uploading multiple kmer histograms at once so it is much more complicated than your code snippet, but glad to see you can generate it on your own. I think it is also a research question to determine when this helpful -- in our tests we try to use the shortest kmer length that is expected to be unique in the genome (usually 21mers) since longer kmers are more likely to overlap multiple errors and/or heterozygous sites which obscures their true frequency. The model tries to accommodate for this by assuming a steady rate of errors & heterozygosity in those regions but it helps to have more information. We are in the process of rebuilding the whole process to support more complicated genomes so will keep this in mind.

Cheers

Mike

On Thu, Feb 15, 2018 at 6:12 AM, Martin Mokrejš notifications@github.com wrote:

I was downloading a URL like the http://qb.cshl.edu/ genomescope/analysis.php?code=UyWTAXyzTJK6mHZPnqxh . Would there be a hyperlink from the page to plot.png and plot.log.png I could have fetched just that too.

Yeah, I went better to fetch the 474MB of genomescope.git and ran the command locally. I haven't realized before you always re-create the results page on the fly. Hmm, that complicates the situation admittedly.

An animated GIF could have been created using convert (part of ImageMagick):

figures=find . -name plot.png | sort | while read f; do echo -n "$f "; done figure_series=for a in $figures; do printf -- "-delay 1000 %s " $a; done convert "$figure_series" animation.gif

The sort step could be improved to do natural type of sorting, but you get the point.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/schatzlab/genomescope/issues/6#issuecomment-365896676, or mute the thread https://github.com/notifications/unsubscribe-auth/AAL98-_04RvGvXllP3PsYKIkIlHaWJ4gks5tVBE3gaJpZM4SCD1c .

[mschatz]

Also, "Save Image As" works for me for your results in Chrome, Firefox, and Safari: http://qb.cshl.edu/genomescope/analysis.php?code=UyWTAXyzTJK6mHZPnqxh

Must be an issue on your side.

Good luck!

Mike

[mmokrejs]

"Save Image As" of course works, but "Save Page As" does not.

[mschatz]

Please try again, works for me (left: CSHL server, right: local machine)

Good luck!

Mike