In the KEGG website, I've downloaded a KGML file which contains all informations of a pathway. But I want to get the vector graphic of the pathway such as SVG file.
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Something like that is likely coming to Biopython, probably in the next release:
This pull request is mainly as a discussion point for Leighton's (@widdowquinn) KEGG KGML parser and visualisation work, originally on the following pull request, but the branch was a little messed...
Leighton's blog posts about this work:
In which I attempt to visualise metabolic maps for comparative genomics, and lead up to making a contribution to Biopython.
In which I don't quite get around to writing a KGML parser and visualisation module (all very Tristram Shandy , this!), with a view to submi...
In which I finally get around to sharing some code, and give some examples of downloading and modifying KEGG pathway maps.
This using Python to parse the KGML XML files, which can then be rendered using the manual layout positions KEGG provide. The examples produce PDF, but underneath this uses the ReportLab library for the graphics which supports vector output including PDF and SVG (and also bitmap output like PNG) so using this for SVG output should in principle be possible.
You can also overlay this information on top of the template PNG images KEGG provide to make annotated variations, for example to emphasise a particular pathway.
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Originally posted by maubp View PostSomething like that is likely coming to Biopython, probably in the next release:
This pull request is mainly as a discussion point for Leighton's (@widdowquinn) KEGG KGML parser and visualisation work, originally on the following pull request, but the branch was a little messed...
Leighton's blog posts about this work:
In which I attempt to visualise metabolic maps for comparative genomics, and lead up to making a contribution to Biopython.
In which I don't quite get around to writing a KGML parser and visualisation module (all very Tristram Shandy , this!), with a view to submi...
In which I finally get around to sharing some code, and give some examples of downloading and modifying KEGG pathway maps.
This using Python to parse the KGML XML files, which can then be rendered using the manual layout positions KEGG provide. The examples produce PDF, but underneath this uses the ReportLab library for the graphics which supports vector output including PDF and SVG (and also bitmap output like PNG) so using this for SVG output should in principle be possible.
You can also overlay this information on top of the template PNG images KEGG provide to make annotated variations, for example to emphasise a particular pathway.
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