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

package test::role;

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

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

coerce 'ModNum',

sestaton

use strict;
use warnings;

my ($def, $seq);

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

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

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

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

# -*- coding: utf-8 -*-
module SequenceServer
  # Module to contain methods for generating sequence retrieval links.
  module Links
    require 'erb'

    include ERB::Util

    alias_method :encode, :url_encode

sestaton

from ftplib import FTP

host = "ftp.ncbi.nlm.nih.gov"
wdir = "/genomes/refseq/"

ftp = FTP(host, 'anonymous', 'anonymous')
ftp.set_pasv(1)

list = ftp.nlst(wdir)
print len(list)

sestaton

use strict;
use warnings;
use Net::FTP;

my $host = "ftp.ncbi.nlm.nih.gov";
my $wdir = "/genomes/refseq/";

my $ftp = Net::FTP->new($host, Passive => 1, Debug => 0)
    or die "Cannot connect to $host: $@";

sestaton

# always include these lines! (implicit in recent Perl versions)
use strict;   # follow the rules
use warnings; # warning when we make a mistake

# import method to perform the request
use LWP::UserAgent;

# make the format an option perhaps
my $format  = 'fasta';
my $urlbase = 'http://www.uniprot.org/uniprot/';