function parser_ipi_OSCODE_xref_gz_file($anInputPath, $anOSCODEFile, $outputPath)
{
//check if inputpath has a trailing slash
if (strrpos($anInputPath, "/") != count($anInputPath)) {
//no trailing slash
$anInputPath .= "/";
}
if (strrpos($outputPath, "/") != count($outputPath)) {
//no trailing slash
$outputPath .= "/";
}
echo "Processing {$anInputPath}, {$anOSCODEFile}, {$outputPath} " . PHP_EOL;
$out_fileName = substr($anOSCODEFile, 0, strrpos($anOSCODEFile, "."));
$ifh = gzopen($anInputPath . $anOSCODEFile, 'r') or die("Could not open " . $anInputPath . $anOSCODEFile . "\n");
$outfh = fopen($outputPath . $out_fileName . ".nt", 'w') or die("Could not open file here!\n");
if ($ifh) {
while (!gzeof($ifh)) {
$aLine = gzgets($ifh, 4096);
$tLine = explode("\t", $aLine);
//see http://www.ebi.ac.uk/IPI/xrefs.html
//get the Database from which master entry of this IPI entry has been taken.
$master_db = null;
//key is code, value is bio2rdf namespace
if ($tLine[0] == "SP" || $tLine[0] == "REFSEQ_REVIEWED" || $tLine[0] == "TR" || $tLine[0] == "ENSEMBL" || $tLine[0] == "ENSEMBL_HAVANA" || $tLine[0] == "REFSEQ_STATUS" || $tLine[0] == "VEGA" || $tLine[0] == "TAIR" || $tLine[0] == "HINV") {
if ($tLine[0] == "SP") {
$master_db["SP"] = "swissprot";
}
if ($tLine[0] == "TR") {
$master_db["TR"] = "uniprot";
}
if ($tLine[0] == "ENSEMBL") {
$master_db["ENSEMBL"] = "ensembl";
}
if ($tLine[0] == "ENSEMBL_HAVANA") {
$master_db["ENSEMBL_HAVANA"] = "ensembl";
}
if ($tLine[0] == "REFSEQ_STATUS") {
$master_db["REFSEQ_STATUS"] = "refseq";
}
if ($tLine[0] == "VEGA") {
$master_db["VEGA"] = "vega";
}
if ($tLine[0] == "TAIR") {
$master_db["TAIR"] = "tair";
}
if ($tLine[0] == "HINV") {
$master_db["HINV"] = "hinv";
}
}
$ipi_id = null;
$sup_uniprots_sps = array();
$uniprotkb_id = null;
$sup_uniprots_tre = array();
$sup_ensembl = array();
$sup_refseq = array();
$sup_tair = array();
$sup_hinv = array();
$xref_embl_genbank_ddbj = array();
$hgnc_ids = array();
$ncbi_ids = array();
$uniparc_ids = array();
$unigene_ids = array();
$ccds_ids = array();
$refseq_gis = array();
$vega_ids = array();
//UniProtKB accession number or Vega ID or Ensembl ID or RefSeq ID or TAIR Protein ID or H-InvDB ID
if (count(isset($tLine[1]))) {
@($uniprotkb_id = getFirstId($tLine[1]));
}
//ipi id
if (count(isset($tLine[2]))) {
@($ipi_id = $tLine[2]);
}
//Supplementary UniProtKB/Swiss-Prot entries associated with this IPI entry.
if (count(isset($tLine[3]))) {
@($sup_uniprots_sps = readIdentifiers($tLine[3]));
}
//Supplementary UniProtKB/TrEMBL entries associated with this IPI entry.
if (count(isset($tLine[4]))) {
@($sup_uniprots_tre = readIdentifiers($tLine[4]));
}
//Supplementary Ensembl entries associated with this IPI entry. Havana curated transcripts preceeded by the key HAVANA: (e.g. HAVANA:ENSP00000237305;ENSP00000356824;).
if (count(isset($tLine[5]))) {
@($sup_ensembl = readIdentifiers($tLine[5]));
}
//Supplementary list of RefSeq STATUS:ID couples (separated by a semi-colon ';') associated with this IPI entry (RefSeq entry revision status details).
if (count(isset($tLine[6]))) {
@($sup_refseq = readIdentifiers($tLine[6]));
}
//Supplementary TAIR Protein entries associated with this IPI entry.
if (count(isset($tLine[7]))) {
@($sup_tair = readIdentifiers($tLine[7]));
}
//Supplementary H-Inv Protein entries associated with this IPI entry.
if (count(isset($tLine[8]))) {
@($sup_hinv = readIdentifiers($tLine[8]));
}
//Protein identifiers (cross reference to EMBL/Genbank/DDBJ nucleotide databases).
if (count(isset($tLine[9]))) {
@($xref_embl_genbank_ddbj = readIdentifiers($tLine[9]));
}
//List of HGNC number, HGNC official gene symbol couples (separated by by a semi-colon ';') associated with this IPI entry.
if (count(isset($tLine[10]))) {
@($hgnc_ids = readIdentifiers($tLine[10]));
}
////List of NCBI Entrez Gene gene number, Entrez Gene Default Gene Symbol couples (separated by a semi-colon ';') associated with this IPI entry.
if (count(isset($tLine[11]))) {
@($ncbi_ids = readIdentifiers($tLine[11]));
}
//UNIPARC identifier associated with the sequence of this IPI entry.
if (count(isset($tLine[12]))) {
@($uniparc_ids = readIdentifiers($tLine[12]));
}
//UniGene identifiers associated with this IPI entry.
if (count(isset($tLine[13]))) {
@($unigene_ids = readIdentifiers($tLine[13]));
}
//CCDS identifiers associated with this IPI entry.
if (count(isset($tLine[14]))) {
@($ccds_ids = readIdentifiers($tLine[14]));
}
//RefSeq GI protein identifiers associated with this IPI entry.
if (count(isset($tLine[15]))) {
@($refseq_gis = readIdentifiers($tLine[15]));
}
//Supplementary Vega entries associated with this IPI entry.
if (count(isset($tLine[16]))) {
@($vega_ids = readIdentifiers($tLine[16]));
}
//now lets print some rdf
$entryURI = "http://bio2rdf.org/ipi:" . $ipi_id;
$buf = "";
if (count($sup_refseq)) {
foreach ($sup_refseq as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_refseq_id> <http://bio2rdf.org/refseq:" . $r . "> .\n";
}
}
}
if ($uniprotkb_id != "" && $uniprotkb_id != "\n" && count($uniprotkb_id) > 1 && isset($uniprotkb_id)) {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_uniprot_id> <http://bio2rdf.org/uniprot:" . $r . "> .\n";
}
if (count($sup_uniprots_sps)) {
foreach ($sup_uniprots_sps as $r) {
if ($r != "" && $r != "\n" && count($r) > 1 && isset($r)) {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_uniprot_id> <http://bio2rdf.org/uniprot:" . $r . "> .\n";
}
}
}
if (count($sup_uniprots_tre)) {
foreach ($sup_uniprots_tre as $r) {
if ($r != "" && $r != "\n" && count($r) > 1 && isset($r)) {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_uniprot_id> <http://bio2rdf.org/uniprot:" . $r . "> .\n";
}
}
}
if (count($sup_ensembl)) {
foreach ($sup_ensembl as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_ensembl_id> <http://bio2rdf.org/ensembl:" . $r . "> .\n";
}
}
}
if (count($sup_tair)) {
foreach ($sup_tair as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_tair_id> <http://bio2rdf.org/tair:" . $r . "> .\n";
}
}
}
if (count($sup_hinv)) {
foreach ($sup_hinv as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_hinv_id> <http://bio2rdf.org/hinv:" . $r . "> .\n";
}
}
}
if (count($xref_embl_genbank_ddbj)) {
foreach ($xref_embl_genbank_ddbj as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_embl_id> <http://bio2rdf.org/embl:" . $r . "> .\n";
}
}
}
if (count($hgnc_ids)) {
foreach ($hgnc_ids as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_hgnc_id> <http://bio2rdf.org/hgnc:" . $r . "> .\n";
}
}
}
if (count($ncbi_ids)) {
foreach ($ncbi_ids as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_gene_id> <http://bio2rdf.org/gene:" . $r . "> .\n";
}
}
}
if (count($uniparc_ids)) {
foreach ($uniparc_ids as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_uniparc_id> <http://bio2rdf.org/uniparc:" . $r . "> .\n";
}
}
}
if (count($unigene_ids)) {
foreach ($unigene_ids as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_unigene_id> <http://bio2rdf.org/unigene:" . $r . "> .\n";
}
}
}
if (count($ccds_ids)) {
foreach ($ccds_ids as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_ccds_id> <http://bio2rdf.org/ccds:" . $r . "> .\n";
}
}
}
if (count($refseq_gis)) {
foreach ($refseq_gis as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_gene_id> <http://bio2rdf.org/gene:" . $r . "> .\n";
}
}
}
if (count($vega_ids)) {
foreach ($vega_ids as $r) {
if ($r != "" && $r != "\n") {
$buf .= "<{$entryURI}> <http://bio2rdf.org/ipi_vocabulary:has_vega_id> <http://bio2rdf.org/vega:" . $r . "> .\n";
}
}
}
fwrite($outfh, $buf);
}
//while
}
//if
if (!feof($ifh)) {
echo "Error: unexpected gzgets() fail!\n";
}
gzclose($ifh);
fclose($outfh);
}
private function gene_xrefs()
{
while ($aLine = $this->getReadFile()->Read(4096)) {
$tLine = explode("\t", $aLine);
if (!$this->startsWith($tLine[0], "#")) {
$chromosome = null;
$cosmid = array();
$start_coord = null;
$gene_symbol = null;
$end_coord = null;
$strand = array();
$gene_location = array();
$ensembl_id = array();
$gene_id = null;
$ipi_ids = array();
$uniprotkb_ids = array();
$uniprot_tre = array();
$ensembl_peptide_id = array();
$refseq_ids = array();
$tair_ids = array();
$hinv_ids = array();
$unigene_ids = array();
$ccds_ids = array();
$refseq_gis = array();
$vega_genes = array();
$vega_peptides = array();
if (count(isset($tLine[0]))) {
@($chr_arr = readIdentifiers($tLine[0]));
if ($chr_arr[0] != "Un") {
$chromosome = $chr_arr[0];
}
}
if (count(isset($tLine[1]))) {
@($cosmid = readIdentifiers($tLine[1]));
}
if (count(isset($tLine[2]))) {
@($start_coord_t = readIdentifiers($tLine[2]));
if (count($start_coord_t) == 1) {
$start_coord = $start_coord_t[0];
}
}
if (count(isset($tLine[3]))) {
@($end_coord_t = readIdentifiers($tLine[3]));
if (count($end_coord_t) == 1) {
$end_coord = $end_coord_t[0];
}
}
if (count(isset($tLine[4]))) {
@($strand = readIdentifiers($tLine[4]));
}
if (count(isset($tLine[5]))) {
@($gene_location = readIdentifiers($tLine[5]));
}
if (count(isset($tLine[6]))) {
@($ensembl_id = readIdentifiers($tLine[6]));
}
if (count(isset($tLine[8]))) {
@($gene_id_t = readIdentifiers($tLine[8]));
if (count($gene_id_t) == 2) {
$gene_id = $gene_id_t[0];
$gene_symbol = $gene_id_t[1];
}
}
if (count(isset($tLine[9]))) {
@($ipi_ids = readIdentifiers($tLine[9]));
}
if (count(isset($tLine[10]))) {
@($uniprotkb_ids = readIdentifiers($tLine[10]));
}
if (count(isset($tLine[11]))) {
@($uniprot_tre = readIdentifiers($tLine[11]));
}
if (count(isset($tLine[12]))) {
@($ensembl_peptide_id = readIdentifiers($tLine[12]));
}
if (count(isset($tLine[13]))) {
@($refseq_ids = readIdentifiers($tLine[13]));
}
if (count(isset($tLine[14]))) {
@($tair_ids = readIdentifiers($tLine[14]));
}
if (count(isset($tLine[15]))) {
@($hinv_ids = readIdentifiers($tLine[15]));
}
if (count(isset($tLine[16]))) {
@($unigene_ids = readIdentifiers($tLine[16]));
}
if (count(isset($tLine[17]))) {
@($ccds_ids = readIdentifiers($tLine[17]));
}
if (count(isset($tLine[18]))) {
@($refseq_gis = readIdentifiers($tLine[18]));
}
if (count(isset($tLine[19]))) {
@($vega_genes = readIdentifiers($tLine[19]));
}
if (count(isset($tLine[20]))) {
@($refseq_ids = readIdentifiers($tLine[20]));
}
//lets make some RDF
if (count($gene_id)) {
$res = "gene:" . $gene_id;
parent::AddRDF(parent::triplifyString($res, $this->getVoc() . "gene-symbol", $gene_symbol) . parent::triplifyString($res, $this->getVoc() . "chromosome", $chromosome) . parent::triplifyString($res, $this->getVoc() . "start-coordinate", $start_coord) . parent::triplifyString($res, $this->getVoc() . "end-coordinate", $end_coord));
}
if (count($strand)) {
parent::AddRDF(parent::triplifyString($res, $this->getVoc() . "strand", $strand[0]));
}
if (count($ensembl_id)) {
foreach ($ensembl_id as $x) {
parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-ensembl", "ensembl:" . $x));
}
}
if (count($gene_location)) {
foreach ($gene_location as $x) {
parent::AddRDF(parent::triplifyString($res, $this->getVoc() . "gene-location", $x));
}
}
if (count($ipi_ids)) {
foreach ($ipi_ids as $x) {
parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-ipi", "ipi:" . $x));
}
}
if (count($uniprotkb_ids)) {
foreach ($uniprotkb_ids as $x) {
parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-uniprot", "uniprot:" . $x));
}
}
if (count($uniprotkb_tre)) {
foreach ($uniprotkb_tre as $x) {
parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-uniprot", "uniprot:" . $x));
}
}
if (count($ensembl_peptide_id)) {
foreach ($ensembl_peptide_id as $x) {
parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-ensembl", "ensembl:" . $x));
}
}
if (count($refseq_ids)) {
foreach ($refseq_ids as $x) {
parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-refseq", "refseq:" . $x));
}
}
if (count($tair_ids)) {
foreach ($tair_ids as $x) {
parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-tair", "tair:" . $x));
}
}
if (count($hinv_ids)) {
foreach ($hinv_ids as $x) {
parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-hinv", "hinv:" . $x));
}
}
if (count($unigene_ids)) {
foreach ($unigene_ids as $x) {
parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-unigene", "unigene:" . $x));
}
}
if (count($refseq_gis)) {
foreach ($refseq_gis as $x) {
if (count($x) != 0 && $x != "\n" && $x != "") {
parent::AddRDF(parent::triplify($res, $this->getVoc() . "x-refseq", "refseq:" . $x));
}
}
}
$this->WriteRDFBufferToWriteFile();
}
}
}
