sestaton

##info1
##info2
##info3
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NAD58	NAD93	NAD98
3   66894   rs9681213   0   1   .   PASS    .   GT  0|1 0|1 0|1 etc...
3   95973   rs1400176   0   1   .   PASS    .   GT  1|1 1|1 1|1 etc...
3   104972  rs990284    0   1   .   PASS    .   GT  0|1 0|1 0|0 etc...
3   114133  rs954824    0   1   .   PASS    .   GT  1|1 1|1 1|1 etc...

sestaton

NAD15
NAD54 
NAD55 
NAD56 
NAD57 
NAD58 
NAD59 
NAD64
NAD93  
NAD98

sestaton

use 5.010;
use strict;
use warnings;
use autodie;
use List::MoreUtils qw(indexes);

my $usage = "$0 ids vcf";
my $ids = shift or die $usage;
my $vcf = shift or die $usage;

sestaton

## For more information about this file, see: 
## https://github.com/sestaton/tephra/wiki/Specifications-and-example-usage.
ltrharvest:
  - mintsd:         4
  - maxtsd:         6
  - minlenltr:      100
  - maxlenltr:      6000
  - mindistltr:     1500
  - maxdistltr:     25000
  - seedlength:     30

sestaton

## For more information about this file, see: 
## https://github.com/sestaton/tephra/wiki/Specifications-and-example-usage.
ltrharvest:
  - mintsd:         4
  - maxtsd:         20
  - minlenltr:      100
  - maxlenltr:      1000
  - mindistltr:     1000
  - maxdistltr:     15000
  - seedlength:     30

sestaton

#!/bin/bash

# set this to the location of muscle and vmatch
export PATH=`pwd`:$PATH

set -euo pipefail

script=$(basename $0)

function usage() {

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/';

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

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

# -*- 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