WARNING: this page is a WORK IN PROGRESS - not for human consumption YET!

An attempt to keep track of all the Perl I've written at the Holmes lab, for posterity.

Disclaimer: "avu" are my initials, but apparently also a file format... do not confuse!

TODO: use InterWiki?

Status	Explanation
	completely finished; no more features planned
	some features could be added
	a lot of features could added; not as robust and/or well-written as I'd like
	the code technically fulfills its described function, but isn't robust (would unelegantly break/behave unexpectedly on malformed input) and/or is just plain badly written

Project-specific

• TwelveFlyScreen
  • do-lg-odds.pl
  • get-hits.pl
  • load-db.pl
  • init-table.pl
• FlyNcRna
  • don't even remember what... need to look in the project's "perl" dir
  • Mapper.pm

General, for lab purposes

TODO: put all these in /nfs/src/perl/ (unless they are already in Dart, or qualify for Dart)

currently in:

• /nfs/src/perl/avu-ncrna-stuff
  • a bunch of stuff... it is a questionably reusable mess, need to organize

already in /nfs/src/perl/, just need to write up a short description here and make sure they're presentable:

• Arguments.pm
• batch.pl
• drop-gappy-cols-aln.pl
• fix-nl.pl
• make-windows.pl
• remdup.pl
• stock2clustalw.pl
• stock2maf.pl
• came from TwelveFlyScreen:
  • rand-cols.pl
  • split-SS_cons.pl
  • get-coord.pl
  • subseq.pl
  • revcomp.pl
• maybe these should go into some sort of "CAF1 scripts" repository?
  • dropForeign.pl
  • gbAccn2caf1.pl
  • gbAccn2name.pl
• wiki-table.pl
  • tips for usage: use regexps for throwing out empties between delimiters, e.g. "\t+" (make sure to use double-quotes in shell) will treat sequences of tabs as a single delimiter, so you don't have empty cells (although if you want that kind of thing, use "\t")

MercatorPerl contribs (should write up on THAT page)

DartPerlScripts

already in:

• drop-gappy-columns.pl
  • dear jeebus I hate this program... just looking at that code makes me want to stab my eyes out... what the hell was I thinking?

need to write

if someone hasn't written it yet... it might be handy to have a robust version of these instead of coming up with stuff on the fly:

• extract a column (given a col num) and return as a line
• count occurence of a char
  • can't grep do this?
    • if it can, it might be useful to get frequency counts...
    • maybe I should dust off good ol' seqmanipulator...
• get specific line #
  • kind of like head -n N | tail -n 1... isn't there a linux command for something like this?
• merge columns
  • should take arbitrary column numbers from arbitrary files (or stdin) and put them in any order
  • for that matter, it's a column rearranger

-- Created by: AndrewUzilov on 28 Mar 2007