Progenetix - Visualizing Cancer Genomics

Master and temporary data files for arrayMap and Progenetix are saved in a JSON format, using Perl’s JSON::XS module. To speed up file I/O, we have deactivated the “pretty” option. This improves file I/O and size by approximately a factor of 2, but makes it rather unreadable. A simple way for reformatting the files (in Perl) would be:

my $json = JSON->new;

open INFILE, $infile;

open OUTFILE, “>”.$outfile;

print OUTFILE JSON::XS->new->pretty( 1 )->encode( $json->decode( <INFILE> ) );

close INFILE;

close OUTFILE;

Also, due to a comment by Felix Kokocinski, we removed a bug where wrongly formatted links (“http:/www. …”) lead to missing image files in the locus score function. The incomplete address is interpolated by Safari, but breaks in Firefox. Thanks!

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Progenetix/arrayMap JSON format update, and a bug fix