radaniba

from xml.etree import ElementTree as ET
import re

def strip_whitespace(my_string):
    """Removes spaces, tabs, and newline characters from a string.
    \s matches any whitespace character, this is equivalent to the class [\t\n\r\f\v]."""
    return re.sub("\s", "", my_string)

my_xml = """
<root>

radaniba

#!/usr/bin/env python

# Run with no args for usage instructions
#
# Notes:
#  - will probably insert duplicate records if you load the same file twice
#  - assumes that the number of fields in the header row is the same
#    as the number of columns in the rest of the file and in the database
#  - assumes the column order is the same in the file and in the database
#

radaniba

if (!function_exists('mysql_search')) {

   function mysql_search($table, $columns, $query = '', $options = Array()) {

      if (empty($query)) { return Array(); }

      $sql_query = Array();

      $options['columns'] = isset($options['columns'])?$options['columns']:'*';
      $options['method'] = isset($options['method'])?$options['method']:'OR';

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if (!function_exists('mysql_search')) {

   function mysql_search($table, $columns, $query = '', $options = Array()) {

      if (empty($query)) { return Array(); }

      $sql_query = Array();

      $options['columns'] = isset($options['columns'])?$options['columns']:'*';
      $options['method'] = isset($options['method'])?$options['method']:'OR';

radaniba

if (!function_exists('mysql_dump')) {
 
   function mysql_dump($database) {
 
      $query = '';
 
      $tables = @mysql_list_tables($database);
      while ($row = @mysql_fetch_row($tables)) { $table_list[] = $row[0]; }
 
      for ($i = 0; $i < @count($table_list); $i++) {

radaniba

from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from Bio import Entrez
from Bio import SeqIO
import time

# Obtain your gene IDs from somewhere (file, past text directly, etc.)
ids = []
ids = ",".join( lines )

radaniba

#!/usr/bin/ruby
# Read in a fast file and spit it out as tipdate

### IMPORTS

require 'test/unit/assertions'
require 'pp'
require 'csv'
require 'bio'
include Test::Unit::Assertions

radaniba

#!/usr/bin/env ruby
# Draw a sequence logo in SVG.

### IMPORTS

require 'test/unit/assertions'
require 'optparse'
require 'pp'
require 'csv'
require 'ostruct'

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public static void main(String[] args) {
        if (args.length != 1) {
            System.out.println("The program expects one parameter: \n"
                    + "1. Protein accesion\n");
        } else {

            String inputSt = args[0];

            Bio4jManager manager = null;

radaniba

#! usr/bin/perl

use warnings;
use strict;

my $gwas_file=$ARGV[0];
my $hugenet_file=$ARGV[1];

my $num_args = $#ARGV + 1;