Andrew Uzilov Perl

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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
TWikiDocGraphics.choice-yes.gifTWikiDocGraphics.choice-yes.gifTWikiDocGraphics.choice-yes.gifTWikiDocGraphics.choice-yes.gif completely finished; no more features planned
TWikiDocGraphics.choice-yes.gifTWikiDocGraphics.choice-yes.gifTWikiDocGraphics.choice-yes.gif some features could be added
TWikiDocGraphics.choice-yes.gifTWikiDocGraphics.choice-yes.gif a lot of features could added; not as robust and/or well-written as I'd like
TWikiDocGraphics.choice-yes.gif 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)

Dart Perl Scripts

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

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-- Created by: Andrew Uzilov on 28 Mar 2007