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feat: Updated 1 files
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@sweep-ai
sweep-ai[bot] committed May 14, 2024
1 parent bdab1c6 commit 146f733
Showing 1 changed file with 92 additions and 142 deletions.
234 changes: 92 additions & 142 deletions src/Resources.php
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Original file line number Diff line number Diff line change
Expand Up @@ -32,71 +32,7 @@ public function __construct($resources_dir = 'resources')
parent::__construct($resources_dir = $resources_dir);
}

// public function get_all_resources()
// {
// $resources = array( );
// $resources[
// "genetic_map_HapMapII_GRCh37"
// ] = $this->get_genetic_map_HapMapII_GRCh37();
// $resources["cytoBand_hg19"] = $this->get_cytoBand_hg19();
// $resources["knownGene_hg19"] = $this->get_knownGene_hg19();
// $resources["kgXref_hg19"] = $this->get_kgXref_hg19();
// return $resources;
// }
// /**
// * Function to get a genetic map based on the given map name
// *
// * @param string $genetic_map - Name of the genetic map to retrieve
// * @return array - Returns an array containing the genetic map
// */
// public function get_genetic_map(string $genetic_map): array
// {
// // Define an array of valid genetic map names
// $valid_genetic_maps = [
// "HapMap2",
// "ACB",
// "ASW",
// "CDX",
// "CEU",
// "CHB",
// "CHS",
// "CLM",
// "FIN",
// "GBR",
// "GIH",
// "IBS",
// "JPT",
// "KHV",
// "LWK",
// "MKK",
// "MXL",
// "PEL",
// "PUR",
// "TSI",
// "YRI",
// ];

// // Check if the given genetic map is valid
// if (!in_array($genetic_map, $valid_genetic_maps, true)) {
// error_log("Invalid genetic map");
// return [];
// }

// // If given genetic map is "HapMap2", retrieve the genetic map using another function
// if ($genetic_map === "HapMap2") {
// return $this->get_genetic_map_HapMapII_GRCh37();
// }

// // If given genetic map is not "HapMap2", retrieve the genetic map using another function
// return $this->get_genetic_map_1000G_GRCh37($genetic_map);
// }

// /**
// * Function to get the HapMap2 genetic map in GRCh37 format
// *
// * @return array - Returns an array containing the HapMap2 genetic map in GRCh37 format
// */
// public function get_genetic_map_HapMapII_GRCh37(): array
// {
// // Check if the current genetic map is already HapMap2
// if ($this->_genetic_map_name !== "HapMap2") {
Expand Down Expand Up @@ -133,22 +69,21 @@ public function __construct($resources_dir = 'resources')
// return $this->_genetic_map;
// }

// /**
// * Returns the cytogenetic banding information for the hg19 reference genome.
// *
// * @return array The cytogenetic banding information for hg19.
// */
// public function get_cytoBand_hg19(): array
// {
// // Check if the cytogenetic banding information for hg19 is already loaded
// if (empty($this->_cytoBand_hg19)) {
// // If not, load the cytogenetic banding information from file
// $this->_cytoBand_hg19 = $this->_loadCytoBand(path: $this->_getPathCytoBandHg19());
// }
/**
* Returns the cytogenetic banding information for the hg19 reference genome.
*
* @return array The cytogenetic banding information for hg19.
*/
public function getCytoBandHg19(): array
{
// Check if the cytogenetic banding information for hg19 is already loaded
if (empty($this->_cytoBand_hg19)) {
// If not, load the cytogenetic banding information from file
$this->_cytoBand_hg19 = $this->loadCytoBand($this->getPathCytoBandHg19());
}

// // Return the loaded cytogenetic banding information for hg19
// return $this->_cytoBand_hg19;
// }
return $this->_cytoBand_hg19;
}

// /**
// * Returns the knownGene_hg19 data.
Expand All @@ -167,22 +102,23 @@ public function __construct($resources_dir = 'resources')
// return $this->_knownGene_hg19;
// }

// /**
// * Returns the kgXref_hg19 data.
// *
// * @return array The kgXref_hg19 data.
// */
// public function get_kgXref_hg19() {
// // Check if the _kgXref_hg19 property is empty.
// if ($this->_kgXref_hg19->empty()) {
// // If it is empty, load the kgXref_hg19 data from the file path.
// $this->_kgXref_hg19 = $this->_load_kgXref(
// $this->_get_path_kgXref_hg19()
// );
// }
// // Return the kgXref_hg19 data.
// return $this->_kgXref_hg19;
// }
/**
* Returns the kgXref data for the hg19 reference genome.
*
* @return array The kgXref data for hg19.
*/
public function getKgXrefHg19(): array
{
// Check if the _kgXref_hg19 property is empty.
if (empty($this->_kgXref_hg19)) {
// If it is empty, load the kgXref_hg19 data from the file path.
$this->_kgXref_hg19 = $this->loadKgXref(
$this->getPathKgXrefHg19()
);
}

return $this->_kgXref_hg19;
}

// public function _load_genetic_map_HapMapII_GRCh37($filename)
// {
Expand Down Expand Up @@ -212,45 +148,59 @@ public function __construct($resources_dir = 'resources')
// return $genetic_map;
// }

// /**
// * Loads a genetic map from a file in the 1000 Genomes Project format (GRCh37).
// *
// * @param string $filename The path to the file to load.
// * @return array An associative array of genetic maps, keyed by chromosome.
// */
// function _load_genetic_map_1000G_GRCh37($filename) {
// $genetic_map = []; // Initialize an empty array to hold the genetic maps.

// $phar = new PharData($filename); // Create a new PharData object from the file.

// foreach ($phar as $member) { // Loop through each file in the Phar archive.
// $filepath = $member->getPathname(); // Get the path to the file.
/**
* Loads a genetic map from a file in the 1000 Genomes Project format (GRCh37).
*
* @param string $filename The path to the file to load.
* @return array An associative array of genetic maps, keyed by chromosome.
*/
function loadGeneticMap1000GGRCh37($filename)
{
$geneticMap = []; // Initialize an empty array to hold the genetic maps.

// $file = gzopen($filepath, 'r'); // Open the file for reading.
// $header = fgetcsv($file, 0, "\t"); // Read the header row of the CSV file.
$phar = new PharData($filename); // Create a new PharData object from the file.

// $tempFile = []; // Initialize an empty array to hold the data rows.
// while (($data = fgetcsv($file, 0, "\t")) !== false) { // Loop through each row of the CSV file.
// if (count($data) == count($header)) { // Check that the row has the same number of columns as the header.
// $tempFile[] = array_combine($header, $data); // Combine the header and data rows into an associative array.
// }
// }
foreach ($phar as $member) { // Loop through each file in the Phar archive.
$filepath = $member->getPathname(); // Get the path to the file.
$geneticMap = $this->processGeneticMapFile($filepath, $geneticMap);
}

// $df = []; // Initialize an empty array to hold the genetic map data.
// foreach ($tempFile as $row) { // Loop through each row of the data.
// $df[] = [ // Add a new array to the $df array.
// "pos" => $row["Position(bp)"], // Add the position to the array.
// "rate" => $row["Rate(cM/Mb)"], // Add the rate to the array.
// "map" => $row["Map(cM)"], // Add the map to the array.
// ];
// }

// $chrom = explode("-", $member->getFilename())[1]; // Get the chromosome number from the filename.
// $genetic_map[$chrom] = $df; // Add the genetic map data to the $genetic_map array, keyed by chromosome.
// }
return $geneticMap; // Return the $geneticMap array.
}

// return $genetic_map; // Return the $genetic_map array.
// }
/**
* Processes a single genetic map file and adds the data to the $geneticMap array.
*
* @param string $filepath The path to the genetic map file.
* @param array $geneticMap The array to add the genetic map data to.
* @return array The updated $geneticMap array.
*/
function processGeneticMapFile($filepath, $geneticMap)
{
$file = gzopen($filepath, 'r'); // Open the file for reading.
$header = fgetcsv($file, 0, "\t"); // Read the header row of the CSV file.

$tempFile = []; // Initialize an empty array to hold the data rows.
while (($data = fgetcsv($file, 0, "\t")) !== false) { // Loop through each row of the CSV file.
if (count($data) == count($header)) { // Check that the row has the same number of columns as the header.
$tempFile[] = array_combine($header, $data); // Combine the header and data rows into an associative array.
}
}

$df = []; // Initialize an empty array to hold the genetic map data.
foreach ($tempFile as $row) { // Loop through each row of the data.
$df[] = [ // Add a new array to the $df array.
"pos" => $row["Position(bp)"], // Add the position to the array.
"rate" => $row["Rate(cM/Mb)"], // Add the rate to the array.
"map" => $row["Map(cM)"], // Add the map to the array.
];
}

$chrom = explode("-", basename($filepath))[1]; // Get the chromosome number from the filename.
$geneticMap[$chrom] = $df; // Add the genetic map data to the $geneticMap array, keyed by chromosome.

return $geneticMap;
}

// // public function downloadFile($url, $filename, $compress=False, $timeout=30)
// // {
Expand Down Expand Up @@ -355,18 +305,18 @@ public function __construct($resources_dir = 'resources')
// return $kgXref;
// }

// /**
// * Get local path to cytoBand file for hg19 / GRCh37 from UCSC, downloading if necessary.
// *
// * @return string Path to cytoBand_hg19.txt.gz
// */
// public function getPathCytoBandHg19(): string
// {
// return $this->downloadFile(
// 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz',
// 'cytoBand_hg19.txt.gz'
// );
// }
/**
* Get local path to cytoBand file for hg19 / GRCh37 from UCSC, downloading if necessary.
*
* @return string Path to cytoBand_hg19.txt.gz
*/
public function getPathCytoBandHg19(): string
{
return $this->downloadFile(
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz',
'cytoBand_hg19.txt.gz'
);
}

// /**
// * Download file from a given URL if not exists and return its local path.
Expand Down

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