Bioinformatics

i've been trying to learn new stuff in vim, instead of doing same old. recently, i've been using :tabe to edit in tabs. lately, i've been trying the :sp to edit in splits. this set of tricks makes it even nicer: http://www.vim.org/tips/tip.php?tip_id=173 now i can type ctrl+j to move down or ctrl+k to move up a split and have that split maximized. both tabs and split make it simple to yank and paste between files. something for which i had been using the mouse.

so somehow, my previous post on postgres / mysql made reddit , which i happened to be reading yesterday afternoon. i didnt even realize it was my post until following the link. there were a couple harsh comments stating that i found what i wanted to find. ... which were merited given the sensationalist way i presented the results (50%) and the careless use of the term "benchmark". and yes, the config for mySQL was the default. still, i just presented what i found. i was surprised noone commented on the hackish way that i checked to see if it was a protein sequence in perl, rather than mysql--or the coolness of pre-fetching in DBIx (which is available as eager loading or setting lazy=False in the mapper in python's sqlalchemy). re the comments on things to change in the postgresql.conf... i'll try at some point. are there any suggestions for mysql? the machine has 12G ram, 4CPUs. likely, the raid configuration (i dont know how it's set up) is not optimal, but tha...

At my work, we have a large MySQL database (15 MyISAM tables, 21 million rows, 10Gigs size). After seeing the benchmarks showing that Postgres out-performs MySQL on multi-core machines (our new db server has 4 CPU's), I ported the database to PostgreSQL. We have begun using the DBIx perl module since Class::DBI is too sloooow. The DBIx module allows closer access to the generated SQL, and it allows "prefetch"ing which eliminates extra back-and-forth (and object creation) between the server and client. In addition, the connection string is in the script, not in the generated API. This makes it easy to benchmark as all that is required to change between db engines is to change the connection string. Using this script: use CogeX; use strict; # mysql #my $connstr = 'dbi:mysql:genomes:host:3306'; # postgresql my $connstr = 'dbi:Pg:dbname=genomes;host=host;port=5432'; my $s = CoGeX->connect($connstr, 'user', 'pass' ); my $rs = $s->result...

over thanksgiving, i figured it'd be a good hack to solve the jumble . Originally, i tried to do all permutation of letter orders in the word but got confused and just did letter frequency: import sys word = len(sys.argv) > 1 and (sys.argv[1]).strip("\n").lower() or "egaugnal" words = [w.strip("\n").lower() for w in open('/usr/share/dict/web2') if len(w) == len(word)+1] def lfreq(w): wfreq = {} for letter in w: wfreq[letter] = letter in wfreq and wfreq[letter]+1 or 1 return wfreq wfreq = lfreq(word) match = [w for w in words if lfreq(w) == wfreq] print match that will print all matches for the word send in on the command line, assuming your dictionary file is in /usr/share/dict/web2 :-( . I tried for a while to do a recursive permute function which would take a word or list of letters and return all possible permutations: permute('abc') -> ['abc','acb','bca',bac',cba',cab'], which...

this is the AJAX implementation i use: function jfetch(url,t,o) { var req = jfetch.xhr(); req.open("GET",url,true); req.onreadystatechange = function() { if(req.readyState == 4){ var rsp = req.responseText; if(t.constructor == Function) return t.apply(o,[rsp]); t = document.getElementById(t); t[t.value ==undefined ? 'innerHTML': 'value'] = rsp; req = null; } }; req.send(null); } jfetch.xhr = (window.ActiveXObject) ? function(){ return new ActiveXObject("Microsoft.XMLHTTP"); } : function(){ return new XMLHttpRequest()}; it's short, it only checks for the transport (ActiveX or XHR) once, and it takes either an element id or a call back function. and, i can understand it.