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BioPHP - DNA_remove_non_coding

Original code submitted by joseba
Code bellow is covered by GNU GPL v2 license.

Description

Last change: 2010/10/18 17:04 | Edit description | Recent Changes | Original description

Removes non coding characters from DNA sequence. Degenerated nucleotides
are not removed.

Code

Last change: 2010/10/18 17:04 | Edit Code | Recent Changes | Download | Original code

function DNA_remove_non_coding($seq) {
        // change the sequence to upper case
        $seq=strtoupper($seq);
        // replace all X by N (to normalized sequences)
        $seq=preg_replace("/X/","N",$seq);
        // remove non-words (\W), non coding ([^ATGCYRWSKMDVHBN]) and digits (\d) from sequence
        $seq=preg_replace("/\W|[^ATGCYRWSKMDVHBN]|\d/","",$seq);
        return $seq;
}