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micheldumontiermicheldumontier
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Update goa.php
fixed 2 array issues
1 parent 0735cc2 commit f232ac1

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+67
-73
lines changed

1 file changed

+67
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‎goa/goa.php

+67-73
Original file line numberDiff line numberDiff line change
@@ -238,17 +238,12 @@ function process($file){
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239239

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function getAspect($anAspect){
241-
if(count($anAspect)){
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if($anAspect == "F"){
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return "function";
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}elseif($anAspect == "P"){
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return "process";
246-
}elseif($anAspect == "C"){
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return "component";
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}
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}else{
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return null;
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if($anAspect == "F"){
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return "function";
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}elseif($anAspect == "P"){
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return "process";
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}elseif($anAspect == "C"){
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return "component";
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}
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}
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@@ -283,73 +278,72 @@ function getdbURI($db_id, $db_object_id){
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* ["Experimental Evidence Code" => ["Inferred from Experiment", "0000006"]]
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* See: http://www.geneontology.org/GO.evidence.shtml
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**/
286-
function getEvidenceCodeLabelArr($aec){
287-
if(count($aec)){
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//experimental code
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$ec = array(
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"EXP"=> array("Inferred from Experiment","0000006"),
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"IDA"=> array("Inferred from Direct Assay","0000314"),
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"IPI"=> array("Inferred from Physical Interaction","0000021"),
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"IMP"=> array("Inferred from Mutant Phenotype", "0000315"),
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"IGI"=> array("Inferred from Genetic Interaction","0000316"),
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"IEP"=> array("Inferred from Expression Pattern", "0000008")
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);
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$htp = array(
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"HTP" => array("Inferred from High Throughput Experiment",""),
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"HDA" => array("Inferred from High Throughput Direct Assay",""),
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"HMP" => array("Inferred from Hight Throughput Mutant Phenotype",""),
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"HGI" => array("Inferred from High Throughput Genetic Interaction",""),
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"HEP" => array("Inferred from High Throughput Expression Pattern","")
281+
function getEvidenceCodeLabelArr($aec)
282+
{
283+
//experimental code
284+
$ec = array(
285+
"EXP"=> array("Inferred from Experiment","0000006"),
286+
"IDA"=> array("Inferred from Direct Assay","0000314"),
287+
"IPI"=> array("Inferred from Physical Interaction","0000021"),
288+
"IMP"=> array("Inferred from Mutant Phenotype", "0000315"),
289+
"IGI"=> array("Inferred from Genetic Interaction","0000316"),
290+
"IEP"=> array("Inferred from Expression Pattern", "0000008")
304291
);
305292

306-
//computational analysis codes
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$cac = array(
308-
"ISS"=> array("Inferred from Sequence or Structural Similarity","0000027"),
309-
"ISO"=> array("Inferred from Sequence Orthology", "0000201"),
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"ISA"=> array("Inferred from Sequence Alignment", "0000200"),
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"ISM"=> array("Inferred from Sequence Model", "0000202"),
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"IGC"=> array("Inferred from Genomic Context", "0000317"),
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"IBA"=> array("Inferred from Biological aspect of Ancestor","0000318"),
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"IBD"=> array("Inferred from Biological aspect of Desendant", "0000319"),
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"IKR"=> array("Inferred from Key Residues","0000320"),
316-
"IRD"=> array("Inferred from Rapid Divergence","0000321"),
317-
"RCA"=> array("Inferred from Reviewed Computational Analysis","0000245")
318-
);
319-
320-
//author statement codes
321-
$asc = array(
322-
"TAS"=> array("Traceable Author Statement","0000304"),
323-
"NAS"=> array("Non-Traceable Author Statement","0000303")
324-
);
325-
//curator statement codes
326-
$csc = array(
327-
"IC"=> array("Inferred by Curator","0000001"),
328-
"ND"=> array("No biological Data available","0000035")
329-
);
330-
//automatically assigned codes
331-
$aac = array(
332-
"IEA"=>array("Inferred from Electronic Annotation", "0000203")
293+
$htp = array(
294+
"HTP" => array("Inferred from High Throughput Experiment",""),
295+
"HDA" => array("Inferred from High Throughput Direct Assay",""),
296+
"HMP" => array("Inferred from Hight Throughput Mutant Phenotype",""),
297+
"HGI" => array("Inferred from High Throughput Genetic Interaction",""),
298+
"HEP" => array("Inferred from High Throughput Expression Pattern","")
299+
);
300+
301+
//computational analysis codes
302+
$cac = array(
303+
"ISS"=> array("Inferred from Sequence or Structural Similarity","0000027"),
304+
"ISO"=> array("Inferred from Sequence Orthology", "0000201"),
305+
"ISA"=> array("Inferred from Sequence Alignment", "0000200"),
306+
"ISM"=> array("Inferred from Sequence Model", "0000202"),
307+
"IGC"=> array("Inferred from Genomic Context", "0000317"),
308+
"IBA"=> array("Inferred from Biological aspect of Ancestor","0000318"),
309+
"IBD"=> array("Inferred from Biological aspect of Desendant", "0000319"),
310+
"IKR"=> array("Inferred from Key Residues","0000320"),
311+
"IRD"=> array("Inferred from Rapid Divergence","0000321"),
312+
"RCA"=> array("Inferred from Reviewed Computational Analysis","0000245")
333313
);
334314

335-
if(array_key_exists($aec, $ec)){
336-
return array("experimental evidence code"=>$ec[$aec]);
337-
}elseif(array_key_exists($aec, $htp)){
338-
return array("high throughput code"=>$htp[$aec]);
339-
}elseif(array_key_exists($aec, $cac)){
340-
return array("computational analysis code"=>$cac[$aec]);
341-
}elseif(array_key_exists($aec, $asc)){
342-
return array("author statement code"=>$asc[$aec]);
343-
}elseif(array_key_exists($aec, $csc)){
344-
return array("curator statement code"=>$csc[$aec]);
345-
}elseif(array_key_exists($aec, $aac)){
346-
return array("automatically assigned code"=>$aac[$aec]);
347-
}else{
348-
return array("unmapped evidence code"=> $aec);
349-
}
350-
} else {
351-
return null;
315+
//author statement codes
316+
$asc = array(
317+
"TAS"=> array("Traceable Author Statement","0000304"),
318+
"NAS"=> array("Non-Traceable Author Statement","0000303")
319+
);
320+
//curator statement codes
321+
$csc = array(
322+
"IC"=> array("Inferred by Curator","0000001"),
323+
"ND"=> array("No biological Data available","0000035")
324+
);
325+
//automatically assigned codes
326+
$aac = array(
327+
"IEA"=>array("Inferred from Electronic Annotation", "0000203")
328+
);
329+
330+
if(array_key_exists($aec, $ec)){
331+
return array("experimental evidence code"=>$ec[$aec]);
332+
}elseif(array_key_exists($aec, $htp)){
333+
return array("high throughput code"=>$htp[$aec]);
334+
}elseif(array_key_exists($aec, $cac)){
335+
return array("computational analysis code"=>$cac[$aec]);
336+
}elseif(array_key_exists($aec, $asc)){
337+
return array("author statement code"=>$asc[$aec]);
338+
}elseif(array_key_exists($aec, $csc)){
339+
return array("curator statement code"=>$csc[$aec]);
340+
}elseif(array_key_exists($aec, $aac)){
341+
return array("automatically assigned code"=>$aac[$aec]);
342+
}else{
343+
return array("unmapped evidence code"=> $aec);
352344
}
345+
346+
return null;
353347
}
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355349
function parseDate($str){

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