sestaton

fmtDetailValue_Ontology_term : function(goterm) { 
  if (typeof goterm != 'string') { 
    return goterm; 
  } 
  var dbid = goterm.split(':'); 
  var prefix = ''; 
  switch (dbid[0]) { 
    case 'GO': 
    prefix = 'http://amigo.geneontology.org/amigo/medial_search?q=GO:'; 
    break; 

sestaton

fmtDetailValue_Dbxref : function(dbxref) { 
    if (typeof dbxref != 'string') { 
        return dbxref;
    } 
    var dbid = dbxref.split(':'); 
    var prefix = ''; 
    switch (dbid[0]) { 
      case 'InterPro': 
        prefix = 'http://www.ebi.ac.uk/interpro/entry/'; 
        break; 

sestaton

#!/usr/bin/env perl

use strict;
use warnings;
use File::Basename;

my $usage   = "perl ".basename($0)." seqsi.fas seqsj.fas > seqs_out.fas";
my $infilei = shift or die $usage;
my $infilej = shift or die $usage;

sestaton

use strict;
use warnings;

my ($def, $seq);

while (<>) {
    if (/^DEFINITION\s+(\S+.*)$/) {   
	$def = $1;
    }
    if (/^ORIGIN/) {   

sestaton

package test::role;

use Moose::Role;
use Moose::Util::TypeConstraints;

subtype 'ModNum'
    => as 'Num'
    => where { /\_/ || /\d+/ };

coerce 'ModNum',

sestaton

#!/usr/bin/env perl

use 5.020;
use strict;
use warnings;
use Benchmark qw(:all);

my $seq = "ATCG" x 25e6; # 100Mb string
my $count = 10;

sestaton

#!/bin/bash

## fetch the archive
wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR156/SRR1561197/SRR1561197.sra

## extract the pairs
fastq-dump -F --split-files ./SRR1561197.sra

## trim
fastq_quality_filter -i SRR1561197_1.fastq -q 28 -p 100 -Q33 -o SRR1561197_1_filt.fastq

sestaton

#!/usr/bin/env perl

use strict;
use warnings;
use File::Find;
use Bio::Tools::Run::Alignment::Clustalw;

my $dir = 'genes';
my @files;
find( sub {

sestaton

#!/usr/bin/env perl

use 5.010;
use strict;
use warnings;
use Bio::SeqIO;
use List::MoreUtils qw(any);

my @ids = (1, 5, 10); 
my $num = 0; 

sestaton

#!/usr/bin/env perl

use strict;
use warnings;

my $usage = "blastn -outfmt 6 ... | $0 - > blast_msp_recon.txt\n-OR-\n".
    "$0 blasttable.bln > blast_msp_recon.txt\n";
die $usage if !@ARGV;

while (<>) {