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Pierre Lindenbaum
@yokofakun@genomic.social  ·  activity timestamp last week

Playing with XML+XSLT=SVG because I just hate circos.

#bioinformatics #svg #xml #xslt

screenshot of a genomic circular figure.
screenshot of a genomic circular figure.
screenshot of a genomic circular figure.
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Christian Meesters
@rupdecat@fediscience.org replied  ·  activity timestamp last week

@yokofakun cool! Are you planning to release your tool?

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Pierre Lindenbaum
@yokofakun@genomic.social replied  ·  activity timestamp last week

@rupdecat I just wrote a bed2xml tool https://github.com/lindenb/jvarkit/blob/dev/src/main/java/com/github/lindenb/jvarkit/tools/bed2xml/BedToXml.java and then such XML can be converted to SVG with XSLT

eg.: https://gitlab.univ-nantes.fr/pierre.lindenbaum/gazoduc-nf/-/blob/master/src/xsl/cytoband2svg.xsl?ref_type=heads

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