Merge branch 'r5' of https://github.com/bio2rdf/bio2rdf-scripts

Author: micheldumontier

ctd/ctd.php

@@ -121,7 +121,7 @@ function process(){
 			}
 
 			$out_suffix = parent::getParameterValue('output_format');
-			$ofile = "ctd_".$file.".".$out_suffix;
+			$ofile = "bio2rdf-ctd-".str_replace("_","-", $file).".".$out_suffix;
 			$gz = false;
 
 			if(strstr(parent::getParameterValue('output_format'), "gz")) {

goa/goa.php

@@ -65,14 +65,14 @@ function run(){
 			}
 
 			//download file
-			$rfile = $rdir.strtoupper($file)."/".$basefile.".gz";
+			$rfile = $rdir.strtoupper($file)."/goa_".$file.".gaf.gz";
 			if($download == true) {
-				echo "downloading $file".".gz ... ";
+				echo "downloading $file ... ";
 				utils::DownloadSingle($rfile,$lfile);
 			}
 
 			$gz = (strstr(parent::getParameterValue('output_format'),".gz") === FALSE)?false:true;
-			$ofile = $basefile.".".parent::getParameterValue('output_format'); 	
+			$ofile = "bio2rdf-goa-".$file.".".parent::getParameterValue('output_format'); 	
 
 			parent::setReadFile($lfile, TRUE);
 			parent::setWriteFile($odir.$ofile, $gz);
@@ -144,7 +144,7 @@ function process($file){
 				trigger_error("Expected 17 columns, but found ".count($fields),E_USER_ERROR);
 				return false;
 			}
-		
+			#print_r($fields); exit;
 			//get the Go id
 			$db = $fields[0];
 			$id = $fields[1];
@@ -165,10 +165,6 @@ function process($file){
 
 			//entity id
 			$eid = $this->getdbURI($db,$id);
-if(!$eid) {
-print_r($fields);
-continue;
-}
 			parent::addRDF(
 				parent::describeIndividual($eid,$label,parent::getVoc()."GO-Annotation").
  				parent::describeClass(parent::getVoc()."GO-Annotation","GO Annotation").
@@ -198,12 +194,10 @@ function process($file){
 				parent::triplify($eid, parent::getVoc().$rel, "go:".$goid)					
 			);
 
-			$type = key($eco);
 			$aid = parent::getRes().$file."_".($z++);
 			parent::addRDF(
 				parent::describeObjectProperty(parent::getVoc()."go-annotation","GO annotation").
 				parent::triplify($eid, parent::getVoc()."go-annotation", $aid)
-				
 			);
 
 			$cat = parent::getRes().md5($aspect);
@@ -212,7 +206,7 @@ function process($file){
 				parent::describeIndividual($aid, "$id-go:$goid association", parent::getVoc()."GO-Annotation").
 				parent::triplify($aid, parent::getVoc()."target", $eid).
 				parent::triplify($aid, parent::getVoc()."go-term", "go:".$goid).
-				parent::triplify($aid, parent::getVoc()."evidence", "eco:".$eco[$type][1]).
+				parent::triplify($aid, parent::getVoc()."evidence", "eco:".$eco[1]).
 				parent::triplify($aid, parent::getVoc()."go-category", $cat).
 				parent::describeClass($cat,$aspect).
 				parent::triplifyString($aid, parent::getVoc()."assigned-by", $assignedBy)
@@ -278,28 +272,15 @@ function getdbURI($db_id, $db_object_id){
 	 * ["Experimental Evidence Code" => ["Inferred from Experiment", "0000006"]]
 	 * See: http://www.geneontology.org/GO.evidence.shtml
 	 **/
-	function getEvidenceCodeLabelArr($aec)
-	{
+	function getEvidenceCodeLabelArr($aec){
 		//experimental code
 		$ec = array(
 			"EXP"=> array("Inferred from Experiment","0000006"),
 			"IDA"=> array("Inferred from Direct Assay","0000314"),
 			"IPI"=> array("Inferred from Physical Interaction","0000021"),
 			"IMP"=> array("Inferred from Mutant Phenotype", "0000315"),
 			"IGI"=> array("Inferred from Genetic Interaction","0000316"),
-			"IEP"=> array("Inferred from Expression Pattern", "0000008")
-			);
-			
-		$htp = array(			
-			"HTP" => array("Inferred from High Throughput Experiment",""),
-			"HDA" => array("Inferred from High Throughput Direct Assay",""),
-			"HMP" => array("Inferred from Hight Throughput Mutant Phenotype",""),
-			"HGI" => array("Inferred from High Throughput Genetic Interaction",""),
-			"HEP" => array("Inferred from High Throughput Expression Pattern","")
-		);
-		
-		//computational analysis codes
-		$cac = array(
+			"IEP"=> array("Inferred from Expression Pattern", "0000008"),
 			"ISS"=> array("Inferred from Sequence or Structural Similarity","0000027"),
 			"ISO"=> array("Inferred from Sequence Orthology", "0000201"),
 			"ISA"=> array("Inferred from Sequence Alignment", "0000200"),
@@ -309,38 +290,22 @@ function getEvidenceCodeLabelArr($aec)
 			"IBD"=> array("Inferred from Biological aspect of Desendant", "0000319"),
 			"IKR"=> array("Inferred from Key Residues","0000320"),
 			"IRD"=> array("Inferred from Rapid Divergence","0000321"),
-			"RCA"=> array("Inferred from Reviewed Computational Analysis","0000245")
-			);
-			
-			//author statement codes
-		$asc = array(
+			"RCA"=> array("Inferred from Reviewed Computational Analysis","0000245"),
 			"TAS"=> array("Traceable Author Statement","0000304"),
-			"NAS"=> array("Non-Traceable Author Statement","0000303")
-		);
-		//curator statement codes
-		$csc = array(
+			"NAS"=> array("Non-Traceable Author Statement","0000303"),
 			"IC"=> array("Inferred by Curator","0000001"),
-			"ND"=> array("No biological Data available","0000035")
-		);
-		//automatically assigned codes
-		$aac = array(
-			"IEA"=>array("Inferred from Electronic Annotation", "0000203")
-		);
-		
-		if(array_key_exists($aec, $ec)){
-			return array("experimental evidence code"=>$ec[$aec]);
-		}elseif(array_key_exists($aec, $htp)){
-			return array("high throughput code"=>$htp[$aec]);
-		}elseif(array_key_exists($aec, $cac)){
-			return array("computational analysis code"=>$cac[$aec]);
-		}elseif(array_key_exists($aec, $asc)){
-			return array("author statement code"=>$asc[$aec]);
-		}elseif(array_key_exists($aec, $csc)){
-			return array("curator statement code"=>$csc[$aec]);
-		}elseif(array_key_exists($aec, $aac)){
-			return array("automatically assigned code"=>$aac[$aec]);
-		}else{
-			return array("unmapped evidence code"=> $aec);
+			"ND"=> array("No biological Data available","0000035"),
+			"IEA"=>array("Inferred from Electronic Annotation", "0000203"),
+			"HTP" => array("Inferred from High Throughput Experiment",""),
+			"HDA" => array("Inferred from High Throughput Direct Assay",""),
+			"HMP" => array("Inferred from Hight Throughput Mutant Phenotype",""),
+			"HGI" => array("Inferred from High Throughput Genetic Interaction",""),
+			"HEP" => array("Inferred from High Throughput Expression Pattern","")
+		);			
+		if(isset($ec[$aec])) return $ec[$aec];
+		else {
+			trigger_error("No code for $aec");
+			return null;
 		}
 
 		return null;