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Jay Hannah jhannah

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@jhannah
jhannah / gist:202575
Created October 5, 2009 22:49
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 / gist:206358
Created October 9, 2009 20:46
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 / gist:206359
Created October 9, 2009 20:47
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 / gist:206360
Created October 9, 2009 20:49
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 / gist:223096
Created October 31, 2009 14:38
# 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
jhannah / gist:238001
Created November 18, 2009 16:06
=================================
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
jhannah / gist:239941
Created November 21, 2009 01:18
open my $in, "oma_repl_language_text.sql";
open (my $out, ">:encoding(UTF-8)", "utf8.sql");
while (<$in>) {
print $out $_;
}
@jhannah
jhannah / gist:261092
Created December 21, 2009 17:30
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
jhannah / gist:286277
Created January 25, 2010 21:38
#!/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
jhannah / gist:287948
Created January 27, 2010 15:44
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;
}