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

Twelve Fly Screen
- do-lg-odds.pl
- get-hits.pl
- load-db.pl
- init-table.pl
Fly Nc Rna
- 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 Twelve Fly Screen:
- 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")

Mercator Perl contribs (should write up on THAT page)

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?

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

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-- Created by: Andrew Uzilov on 28 Mar 2007