MAKE_DAS_CONF(1p)

💅 MAKE_DAS_CONF — the manual, but make it bestie ✨

ok so the manual name is MAKE_DAS_CONF(1p) and it lives in the User Contributed Perl Documentation section, and literally the whole point of it is that it's a Perl script called make_das_conf.pl and it pulls DAS sources into GBrowse config files. group-chat tutorial time 🎀

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✨ NAME ✨

make_das_conf.pl — the little script that creates GBrowse config files out of DAS sources 🦋

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🌸 SYNOPSIS 🌸

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

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💖 DESCRIPTION 💖

So basically this script generates a rough draft configuration file that's suitable for browsing a remote DAS server. like, a starter pack, not the final fit 🫶

To use it, you hand it the URL of a DAS server. And then it depends on which flavour of URL you give it:

• Point it at the DAS base URL (so, no data source name attached), like http://genome.cse.ucsc.edu/cgi-bin/das — it prints a list of valid data sources to standard output. cute little menu, no cap.
• Give it a complete DAS URL, like http://genome.cse.ucsc.edu/cgi-bin/das/hg16 — it prints a gbrowse configuration file to standard output. slay.

You will probably want to tweak the config file after you generate it. it's a draft, bestie, it's giving first attempt energy 😭 In particular:

• you'll 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. read that again. it's not lying to you, it's just doing its best 💀

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}

periodt. that's the one you want.

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🦋 SEE ALSO 🦋

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

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👑 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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and that's the whole page, bestie 🌈 it came from perl v5.40.0, dated 2024-10-20 — iconic, timeless, a whole era 💅✨