Lincoln D. Stein > GBrowse-2.54 > make_das_conf.pl

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NAME ^

make_das_conf.pl - Create GBrowse config files from DAS sources

SYNOPSIS ^

  % make_das_conf.pl http://genome.cse.ucsc.edu/cgi-bin/das/hg16 > /usr/local/apache/conf/gbrowse.conf/ucsc.conf

DESCRIPTION ^

This script generates a rough draft configuration file suitable for browsing a remote DAS server.

To use this script, give it the URL of a DAS server. If you point it at the DAS base URL (without the data source name), as in "http://genome.cse.ucsc.edu/cgi-bin/das", it will print a list of valid data sources to standard output. If you give it a complete DAS URL, as in "http://genome.cse.ucsc.edu/cgi-bin/das/hg16", it will print a gbrowse configuration file to standard output.

You will probably want to tweak the configuration file after you generate it. In particular, you will want to customize the glyph types associated with each track and adjust the list of examples given in the instructions (by default this script uses the complete list of entry points, which may be rather long).

Also be aware that this script creates a set of aggregators that may or may not be correct. Consider the case of a DAS server which uses the canonical structure for a spliced mRNA:

     main method:   mRNA
     subparts:      5'-UTR, CDS, 3'-UTR

This conversion script will generate the following set of aggregators:

   mRNA{mRNA}
   5'-UTR{5'-UTR}
   CDS{CDS}
   3'-UTR{3'-UTR}

It will also generate a total of four tracks, one each for the mRNA and each of its parts.

This is, of course, incorrect. You will want to consolidate these into a single aggregator:

   mRNA{5'-UTR,3'-UTR,CDS/mRNA}

SEE ALSO ^

Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl

AUTHOR ^

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2002 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.

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