http://www.mediawiki.org/wiki/Special:Code/MediaWiki/73598
Revision: 73598
Author: yaron
Date: 2010-09-23 12:17:35 +0000 (Thu, 23 Sep 2010)
Log Message:
-----------
Added getGFFData() function, to handle GFF data format
Modified Paths:
--------------
trunk/extensions/ExternalData/ED_Utils.php
Modified: trunk/extensions/ExternalData/ED_Utils.php
===================================================================
--- trunk/extensions/ExternalData/ED_Utils.php 2010-09-23 11:07:52 UTC (rev
73597)
+++ trunk/extensions/ExternalData/ED_Utils.php 2010-09-23 12:17:35 UTC (rev
73598)
@@ -265,6 +265,81 @@
}
/**
+ * This function handles version 3 of the genomic-data format GFF,
+ * defined here:
+ * http://www.sequenceontology.org/gff3.shtml
+ */
+ static function getGFFData( $gff ) {
+ // use an fgetcsv() call, similar to the one in getCSVData()
+ // (fgetcsv() can handle delimiters other than commas, in this
+ // case a tab)
+ $fiveMBs = 5 * 1024 * 1024;
+ $fp = fopen( "php://temp/maxmemory:$fiveMBs", 'r+' );
+ fputs( $fp, $gff );
+ rewind( $fp );
+ $table = array();
+ while ( $line = fgetcsv( $fp, null, "\t" ) ) {
+ // ignore comment lines
+ if ( strpos( $line[0], '##' ) !== 0 ) {
+ // special handling for final 'attributes'
column
+ if ( array_key_exists( 8, $line ) ) {
+ $attributes = explode( ';', $line[8] );
+ foreach ( $attributes as $attribute ) {
+ $keyAndValue = explode( '=',
$attribute, 2 );
+ if ( count( $keyAndValue ) == 2
) {
+ $key = strtolower(
$keyAndValue[0] );
+ $value =
$keyAndValue[1];
+ $line[$key] = $value;
+ }
+ }
+ }
+ array_push( $table, $line );
+ }
+ }
+ fclose( $fp );
+ // now "flip" the data, turning it into a column-by-column
+ // array, instead of row-by-row
+ if ( $has_header ) {
+ $header_vals = array_shift( $table );
+ }
+ $values = array();
+ foreach ( $table as $line ) {
+ foreach ( $line as $i => $row_val ) {
+ // each of the columns in GFF have a
+ // pre-defined name - even the last column
+ // has its own name, "attributes"
+ if ( $i === 0 ) {
+ $column = 'seqid';
+ } elseif ( $i == 1 ) {
+ $column = 'source';
+ } elseif ( $i == 2 ) {
+ $column = 'type';
+ } elseif ( $i == 3 ) {
+ $column = 'start';
+ } elseif ( $i == 4 ) {
+ $column = 'end';
+ } elseif ( $i == 5 ) {
+ $column = 'score';
+ } elseif ( $i == 6 ) {
+ $column = 'strand';
+ } elseif ( $i == 7 ) {
+ $column = 'phase';
+ } elseif ( $i == 8 ) {
+ $column = 'attributes';
+ } else {
+ // this is hopefully an attribute key
+ $column = $i;
+ }
+ if ( array_key_exists( $column, $values ) )
+ $values[$column][] = $row_val;
+ else
+ $values[$column] = array( $row_val );
+ }
+ }
+ return $values;
+ }
+
+ /**
* Recursive function for use by getJSONData()
*/
static function parseTree( $tree, &$retrieved_values ) {
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