jhannah

jhannah@klab:~/src/bioperl-live$ perl t/RemoteDB/EUtilities.t
Can't find 'build_params' in _build at /usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1011.
BEGIN failed--compilation aborted at t/RemoteDB/EUtilities.t line 51.

jhannah

jhannah@dev:~/src/Omni2> perl Makefile.PL
include /home/jhannah/src/Omni2/inc/Module/Install.pm
include inc/Module/Install/Metadata.pm
include inc/Module/Install/Base.pm
include inc/Module/Install/DiffCheck.pm
*** Module::Install::DiffCheck
running 'Model/refresh_Schema.pl'
   Dumping manual schema for Omni2::Model::oma::Schema to directory /home/jhannah/src ...
   Schema dump completed.
   Dumping manual schema for Omni2::Model::oma_repl::Schema to directory /home/jhannah/src ...

jhannah

jhannah@dev:~/src/Omni2> perl Makefile.PL
include /home/jhannah/src/Omni2/inc/Module/Install.pm
include inc/Module/Install/Metadata.pm
include inc/Module/Install/Base.pm
include inc/Module/Install/DiffCheck.pm
*** Module::Install::DiffCheck
running 'Model/refresh_Schema.pl'
   Dumping manual schema for Omni2::Model::oma::Schema to directory /home/jhannah/src ...
   Schema dump completed.
   Dumping manual schema for Omni2::Model::oma_repl::Schema to directory /home/jhannah/src ...

jhannah

jhannah@dev:~/src/Omni2> perl Makefile.PL
include /home/jhannah/src/Omni2/inc/Module/Install.pm
include inc/Module/Install/Metadata.pm
include inc/Module/Install/Base.pm
include inc/Module/Install/DiffCheck.pm
*** Module::Install::DiffCheck
running 'Model/refresh_Schema.pl'
   Dumping manual schema for Omni2::Model::oma::Schema to directory /home/jhannah/src ...
   Schema dump completed.
   Dumping manual schema for Omni2::Model::oma_repl::Schema to directory /home/jhannah/src ...

jhannah

# Here's an example of having BioPerl write an alignment into the middle 
# of an HTML stream:

use strict;
use IO::Scalar;
use BIo::AlignIO;

my $html = "<h1>Blah!</h1>\n";
my $html_fh = new IO::Scalar \$html;

jhannah

=================================
What I've learned so far...
=================================
[raymond] says that daily optimize is probably too much. Instead, only run when your data is 'churned'. 
10:33 < deafferret> [raymond]: want to give me a clue about how to know if my data is churned?
10:34 < [raymond]> deafferret: SHOW GLOBAL STATUS LIKE 'Com_%'; -- look through that list, you'll find some interesting data points.



=================================

jhannah

open my $in, "oma_repl_language_text.sql";
open (my $out, ">:encoding(UTF-8)", "utf8.sql");
while (<$in>) {
   print $out $_;
}

jhannah

my $answer;
while (! $answer) {
   $answer = prompt();
}

if ($answer == 1) {
   print "you chose foo\n";
} elsif ($answer == 2) {
   print "you chose bar\n";
} elsif ($answer == 3) {

jhannah

#!/usr/bin/perl

use strict;
use Bio::SeqIO;

my @files = `find /home/obcarter/2010/bacteria/ -name "*.gbk"`;
foreach my $file (@files) {
   chomp $file;
   my $in = Bio::SeqIO->new(-file => $file, -format => 'genbank');
   while (my $seq = $in->next_seq) {

jhannah

my %cities;
open my $in, "infile";
while (<$in>) {
   my @line = split /\t/;
   next unless $line[2] eq "H1N1";
   next unless $line[6] eq "South Africa";
   my @city = split /\//, $line[3];
   $city = $city[1];
   $cities{$city} = 1;
}