{"id":836,"date":"2017-02-23T19:01:41","date_gmt":"2017-02-23T19:01:41","guid":{"rendered":"http:\/\/www.cellbiol.com\/bioinformatics_web_development\/?page_id=836"},"modified":"2017-04-08T17:49:02","modified_gmt":"2017-04-08T17:49:02","slug":"php-programming-language-basics-more-on-strings-and-biological-sequences-manipulation-with-predefined-functions","status":"publish","type":"page","link":"http:\/\/www.cellbiol.com\/bioinformatics_web_development\/chapter-4-adding-a-dynamic-layer-introducing-the-php-programming-language\/php-programming-language-basics-more-on-strings-and-biological-sequences-manipulation-with-predefined-functions\/","title":{"rendered":"4-7: PHP programming language basics – more on strings and biological sequences manipulation with predefined functions"},"content":{"rendered":"

In the previous section we have started to see some basics on how to manipulate strings and biological sequences in PHP<\/a> by using predefined functions. In this section we explore the topic further by exploring a few more useful PHP built-in tools (predefined functions).<\/p>\n

Splitting a biological sequence in single nucleotides, codons or amino-acids with the str_split() function<\/h2>\n

str_split() – string split<\/strong> – requires two arguments, a string and a number (an integer). It allows, as the name suggests, to split a string in pieces composed by a certain number (the second argument passed on function call) of characters. If the passed number exceeds the string length, it will return the entire string. If the string length cannot be exactly divided by the number, it will return sub strings formed by the passed number and a last substring with what remains.<\/p>\n

Let’s make this more clear with a few examples.<\/p>\n

\r\nSplitting 123456789 to substrings of 3 characters
\";\r\nvar_dump($splitted_on_3);\r\necho \"<\/p>\";\r\n\r\n\/\/ Will output: array(3) { [0]=> string(3) \"123\" [1]=> string(3) \"456\" [2]=> string(3) \"789\" }\r\n\r\n$splitted_on_2 = str_split($mystring,2); \/\/ splitting to sub-strings or 2 characters \r\n\r\necho \"
Splitting 123456789 to substrings of 2 characters
\";\r\nvar_dump($splitted_on_2);\r\n\/\/ Will output: array(5) { [0]=> string(2) \"12\" [1]=> string(2) \"34\" [2]=> string(2) \"56\" [3]=> string(2) \"78\" [4]=> string(1) \"9\" }\r\necho \"<\/p>\";\r\n\r\n$splitted_on_10 = str_split($mystring,10); \/\/ splitting to sub-strings or 10 characters \r\n\r\necho \"
Splitting 123456789 to substrings of 10 characters
\";\r\nvar_dump($splitted_on_10);\r\n\/\/ Will output: array(1) { [0]=> string(9) \"123456789\" }\r\necho \"<\/p>\";\r\n\r\n?>\r\n<\/code><\/pre>\n
In the example above please note that when we try to split a 9 characters string in substrings of 2 characters, str_split() will generate an array of 5 elements. The first 4 are composed by substrings of 2 characters (what we asked for by passing 2 as second argument to the function) and the last by just one character, that constitutes the remainder of the string after having taken out all the possible two characters substrings.<\/p>\n
Also note that when we attempt to subdivide our string in substrings longer than the string itself – in this example we try to subdivide a 9 characters string in substrings of 10 – the whole string is returned as the single element of the str_split() output array.<\/p>\n
In the example that follows we use str_split() to subdivide a coding sequence into the codons (triplets) that compose it. You may see as this could be a first step toward a translation of our DNA coding sequence into a protein sequence.<\/p>\n
\r\n\\nHere are the codons composing $cod_sequence<\/strong>\\n