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Sandbox logs for ab67184

Checking src/Snps/IO/Writer.php for syntax errors... ✅ src/Snps/IO/Writer.php has no syntax errors! 1/1 ✓

Checking src/Snps/IO/Writer.php for syntax errors...
✅ src/Snps/IO/Writer.php has no syntax errors!

Sandbox passed on the latest main, so sandbox checks will be enabled for this issue.

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Step 1: 🔎 Searching

I found the following snippets in your repository. I will now analyze these snippets and come up with a plan.

Some code snippets I think are relevant in decreasing order of relevance (click to expand). If some file is missing from here, you can mention the path in the ticket description.

php-dna/src/Snps/IO/Writer.php

Lines 1 to 426 in ac56520

	<?php
	namespace Dna\Snps\IO;
	use Dna\Snps\SNPs;
	use Dna\Snps\SNPsResources;
	use League\Csv\Info;
	use League\Csv\Reader as CsvReader;
	use League\Csv\Statement;
	use php_user_filter;
	use ZipArchive;
	class Writer
	{
	/**
	* Writer constructor.
	*
	* @param SNPs|null $snps SNPs to save to file or write to buffer
	* @param string|resource $filename Filename for file to save or buffer to write to
	* @param bool $vcf Flag to save file as VCF
	* @param bool $atomic Atomically write output to a file on the local filesystem
	* @param string $vcfAltUnavailable Representation of VCF ALT allele when ALT is not able to be determined
	* @param string $vcfChromPrefix Prefix for chromosomes in VCF CHROM column
	* @param bool $vcfQcOnly For VCF, output only SNPs that pass quality control
	* @param bool $vcfQcFilter For VCF, populate VCF FILTER column based on quality control results
	* @param array $kwargs Additional parameters to `pandas.DataFrame.to_csv`
	*/
	public function __construct(
	protected readonly ?SNPs $snps = null,
	protected readonly string|resource $filename = '',
	protected readonly bool $vcf = false,
	protected readonly bool $atomic = true,
	protected readonly string $vcfAltUnavailable = '.',
	protected readonly string $vcfChromPrefix = '',
	protected readonly bool $vcfQcOnly = false,
	protected readonly bool $vcfQcFilter = false,
	protected readonly array $kwargs = []
	) {}
	/**
	* Write SNPs to file or buffer.
	*
	* @return string Path to file in output directory if SNPs were saved, else empty str
	* @return array SNPs with discrepant positions discovered while saving VCF
	*/
	public function write()
	{
	if ($this->_vcf) {
	return $this->_writeVcf();
	} else {
	return [$this->_writeCsv()];
	}
	}
	/**
	* Write SNPs to a file or buffer.
	*
	* @param SNPs|null $snps
	* @param string|resource $filename
	* @param bool $vcf
	* @param bool $atomic
	* @param string $vcfAltUnavailable
	* @param bool $vcfQcOnly
	* @param bool $vcfQcFilter
	* @param array $kwargs
	* @return string|array Path to file in output directory if SNPs were saved, else empty str; or SNPs with discrepant positions discovered while saving VCF
	* @throws DeprecationWarning This method will be removed in a future release.
	*/
	public static function writeFile(
	?SNPs $snps = null,
	$filename = '',
	bool $vcf = false,
	bool $atomic = true,
	string $vcfAltUnavailable = '.',
	bool $vcfQcOnly = false,
	bool $vcfQcFilter = false,
	array $kwargs = []
	) {
	trigger_error(
	"This method will be removed in a future release.",
	E_USER_DEPRECATED
	);
	$w = new self(
	$snps,
	$filename,
	$vcf,
	$atomic,
	$vcfAltUnavailable,
	$vcfQcOnly,
	$vcfQcFilter,
	kwargs: $kwargs
	);
	return $w->write();
	}
	protected function writeCsv()
	{
	/** Write SNPs to a CSV file.
	*
	* @return string Path to file in the output directory if SNPs were saved, else an empty string
	*/
	$filename = $this->_filename;
	if (empty($filename)) {
	$ext = ".txt";
	if (array_key_exists("sep", $this->_kwargs) && $this->_kwargs["sep"] == ",") {
	$ext = ".csv";
	}
	$filename = cleanStr($this->_snps->source) . "_" . $this->_snps->assembly . $ext;
	}
	$comment = "# Source(s): " . $this->_snps->source . "\n"
	. "# Build: " . $this->_snps->build . "\n"
	. "# Build Detected: " . ($this->_snps->build_detected ? "true" : "false") . "\n"
	. "# Phased: " . ($this->_snps->phased ? "true" : "false") . "\n"
	. "# SNPs: " . $this->_snps->count . "\n"
	. "# Chromosomes: " . $this->_snps->chromosomesSummary . "\n";
	if (array_key_exists("header", $this->_kwargs)) {
	if (is_bool($this->_kwargs["header"])) {
	if ($this->_kwargs["header"]) {
	$this->_kwargs["header"] = ["chromosome", "position", "genotype"];
	}
	} else {
	$this->_kwargs["header"] = ["chromosome", "position", "genotype"];
	}
	} else {
	$this->_kwargs["header"] = ["chromosome", "position", "genotype"];
	}
	return saveArrayAsCsv(
	$this->_snps->_snps,
	$this->_snps->_output_dir,
	$filename,
	$comment,
	$this->_atomic,
	$this->_kwargs
	);
	}
	protected function writeVcf()
	{
	/** Write SNPs to a VCF file.
	*
	* @return array Array containing the path to file in output directory if SNPs were saved, else an empty string,
	* and an array representing discrepant positions discovered while saving VCF
	*
	* @see https://samtools.github.io/hts-specs/VCFv4.2.pdf The Variant Call Format (VCF) Version 4.2 Specification
	*/
	$filename = $this->_filename;
	if (empty($filename)) {
	$filename = cleanStr($this->_snps->source) . "_" . $this->_snps->assembly . ".vcf";
	}
	$comment = "##fileformat=VCFv4.2\n"
	. '##fileDate=' . gmdate("Ymd") . "\n"
	. '##source="' . $this->_snps->source . '; snps v' . snpsVersion() . '; https://pypi.org/project/snps/"' . "\n";
	$referenceSequenceChroms = [
	"1", "2", "3", "4", "5", "6", "7", "8", "9", "10",
	"11", "12", "13", "14", "15", "16", "17", "18", "19", "20",
	"21", "22", "X", "Y", "MT"
	];
	$df = $this->_snps->snps;
	$p = $this->_snps->parallelizer;
	$tasks = [];
	// skip insertions and deletions
	$df = $df->drop(
	$df->filter(function ($row) {
	$genotype = $row['genotype'];
	return !empty($genotype) && (strpos($genotype, 'I') === 0 || strpos($genotype, 'D') === 0);
	})->index()
	);
	$chromsToDrop = [];
	foreach ($df['chrom']->unique() as $chrom) {
	if (!in_array($chrom, $referenceSequenceChroms)) {
	$chromsToDrop[] = $chrom;
	continue;
	}
	$tasks[] = [
	'resources' => $this->_snps->resources,
	'assembly' => $this->_snps->assembly,
	'chrom' => $chrom,
	'snps' => $df->filter(function ($row) use ($chrom) {
	return $row['chrom'] === $chrom;
	}),
	'cluster' => ($this->_vcfQcOnly || $this->_vcfQcFilter) ? $this->_snps->cluster : '',
	'low_quality_snps' => ($this->_vcfQcOnly || $this->_vcfQcFilter) ? $this->_snps->low_quality : getEmptySnpsArray(),
	];
	}
	foreach ($chromsToDrop as $chrom) {
	$df = $df->filter(function ($row) use ($chrom) {
	return $row['chrom'] !== $chrom;
	});
	}
	$results = $p([$this, 'createVcfRepresentation'], $tasks);
	$contigs = [];
	$vcf = [];
	$discrepantVcfPosition = [];
	foreach ($results as $result) {
	$contigs[] = $result['contig'];
	$vcf[] = $result['vcf'];
	$discrepantVcfPosition[] = $result['discrepant_vcf_position'];
	}
	$vcf = array_merge([], ...$vcf);
	$discrepantVcfPosition = array_merge([], ...$discrepantVcfPosition);
	$comment .= implode('', $contigs);
	if ($this->_vcfQcFilter && $this->_snps->cluster) {
	$comment .= '##FILTER=<ID=lq,Description="Low quality SNP per Lu et al.: https://doi.org/10.1016/j.csbj.2021.06.040">' . "\n";
	}
	$comment .= '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">' . "\n";
	$comment .= "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE\n";
	return [
	saveArrayAsCsv(
	$vcf,
	$this->_snps->_output_dir,
	$filename,
	$comment,
	false,
	false,
	false,
	".",
	"\t"
	),
	$discrepantVcfPosition,
	];
	}
	protected function computeAlt($ref, $genotype)
	{
	$genotypeAlleles = array_values(array_unique($genotype));
	if (in_array($ref, $genotypeAlleles, true)) {
	if (count($genotypeAlleles) === 1) {
	return $this->_vcfAltUnavailable;
	} else {
	$refIndex = array_search($ref, $genotypeAlleles, true);
	unset($genotypeAlleles[$refIndex]);
	return array_shift($genotypeAlleles);
	}
	} else {
	sort($genotypeAlleles);
	return implode(",", $genotypeAlleles);
	}
	}
	protected function computeGenotype($ref, $alt, $genotype)
	{
	$alleles = [$ref];
	if ($this->_snps->phased) {
	$separator = "|";
	} else {
	$separator = "/";
	}
	if (!is_null($alt)) {
	$alleles = array_merge($alleles, explode(",", $alt));
	}
	if (count($genotype) === 2) {
	return array_search($genotype[0], $alleles, true) . $separator . array_search($genotype[1], $alleles, true);
	} else {
	return array_search($genotype[0], $alleles, true);
	}
	}
	protected function createVcfRepresentation($task)
	{
	$resources = $task["resources"];
	$assembly = $task["assembly"];
	$chrom = $task["chrom"];
	$snps = $task["snps"];
	$cluster = $task["cluster"];
	$lowQualitySnps = $task["low_quality_snps"];
	if (count(array_filter($snps["genotype"]->notnull())) === 0) {
	return [
	"contig" => "",
	"vcf" => [],
	"discrepant_vcf_position" => [],
	];
	}
	$seqs = $resources->getReferenceSequences($assembly, [$chrom]);
	$seq = $seqs[$chrom];
	$contig = sprintf(
	'##contig=<ID=%s,URL=%s,length=%s,assembly=%s,md5=%s,species="%s">' . PHP_EOL,
	$seq->ID,
	$seq->url,
	$seq->length,
	$seq->build,
	$seq->md5,
	$seq->species
	);
	if ($this->_vcfQcOnly && $cluster) {
	// Drop low quality SNPs if SNPs object maps to a cluster
	$snps = array_filter($snps->drop($this->arrayIntersectAssoc($snps->index, $lowQualitySnps->index)));
	}
	if ($this->_vcfQcFilter && $cluster) {
	// Initialize filter for all SNPs if SNPs object maps to a cluster
	$snps["filter"] = "PASS";
	// Then indicate SNPs that were identified as low quality
	foreach ($lowQualitySnps->index as $index) {
	if (isset($snps[$index])) {
	$snps[$index]["filter"] = "lq";
	}
	}
	}
	$snps = array_values($snps);
	$df = [
	"CHROM" => [],
	"POS" => [],
	"ID" => [],
	"REF" => [],
	"ALT" => [],
	"QUAL" => [],
	"FILTER" => [],
	"INFO" => [],
	"FORMAT" => [],
	"SAMPLE" => [],
	];
	// Set data types for the arrays
	$dataTypes = [
	"CHROM" => "object",
	"POS" => "uint32",
	"ID" => "object",
	"REF" => "object",
	"ALT" => "object",
	"QUAL" => "float32",
	"FILTER" => "object",
	"INFO" => "object",
	"FORMAT" => "object",
	"SAMPLE" => "object",
	];
	foreach ($df as $col => $values) {
	$df[$col] = array_fill(0, count($snps), $values);
	}
	foreach ($snps as $index => $row) {
	$df["CHROM"][$index] = $this->_vcfChromPrefix . $row["chrom"];
	$df["POS"][$index] = $row["pos"];
	$df["ID"][$index] = $row["rsid"];
	}
	if ($this->_vcfQcFilter && $cluster) {
	foreach ($snps as $index => $row) {
	$df["FILTER"][$index] = $row["filter"];
	}
	}
	// Drop SNPs with discrepant positions (outside reference sequence)
	$discrepantVcfPosition = [];
	foreach ($snps as $index => $row) {
	if ($row["pos"] - $seq->start < 0 || $row["pos"] - $seq->start > $seq->length - 1) {
	$discrepantVcfPosition[] = $row;
	unset($snps[$index]);
	}
	}
	// Fill REF column based on the sequence data
	foreach ($snps as $index => $row) {
	$df["REF"][$index] = chr($seq->sequence[$row["pos"] - $seq->start]);
	}
	$df["FORMAT"] = "GT";
	$seq->clear();
	foreach ($snps as $index => $row) {
	$df["genotype"][$index] = $row["genotype"];
	}
	$temp = array_filter($df["genotype"], function ($value) {
	return !is_null($value);
	});
	foreach ($temp as $index => $value) {
	$df["ALT"][$index] = $this->_computeAlt($df["REF"][$index], $value);
	}
	$temp = array_filter($df["genotype"], function ($value) {
	return !is_null($value);
	});
	foreach ($temp as $index => $value) {
	$df["SAMPLE"][$index] = $this->_computeGenotype($df["REF"][$index], $df["ALT"][$index], $value);
	}
	foreach ($df["SAMPLE"] as $index => $value) {
	if (is_null($value)) {
	$df["SAMPLE"][$index] = "./.";
	}
	}
	unset($df["genotype"]);
	return [
	"contig" => $contig,
	"vcf" => $df,
	"discrepant_vcf_position" => $discrepantVcfPosition,
	];
	}

I also found the following external resources that might be helpful:

Summaries of links found in the content:

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Step 2: ⌨️ Coding

• Modify src/Snps/IO/Writer.php ! No changes made Edit

Modify src/Snps/IO/Writer.php with contents:
• Review the Python code from the provided GitHub link and identify all functionalities, including file writing, SNP data manipulation, and VCF/CSV formatting.
• For each identified functionality in the Python code, implement an equivalent PHP method within the Writer class. This includes methods for writing SNP data to CSV and VCF formats, handling file I/O operations, and any data manipulation logic specific to SNP data.
• Ensure that all new methods and modifications use PHP 8.3 features where applicable, such as typed properties, match expressions, and nullsafe operator.
• Replace any Python-specific libraries or functions with their PHP equivalents. For example, replace pandas DataFrame operations with appropriate PHP array manipulations or utilize PHP libraries for CSV and VCF file handling.
• If the Python code uses any external libraries for SNP data manipulation or file formatting, identify PHP equivalents or implement the necessary functionality directly in the Writer class or as separate classes within the src/Snps/IO directory.
• Update the constructor and any existing methods in Writer.php to align with the new functionalities and parameters based on the Python code conversion.
• Ensure that all new code follows PHP best practices, including proper error handling, type hinting, and documentation comments.

• Running GitHub Actions for src/Snps/IO/Writer.php ✗ Edit

Check src/Snps/IO/Writer.php with contents:

• Create src/Snps/IO/AdditionalFile.php ✓ 199ae3b Edit

Create src/Snps/IO/AdditionalFile.php with contents:
• If the Python code relies on external files or libraries not directly translatable to existing PHP libraries, create new PHP files to replicate those functionalities. For example, if there's a Python script for parsing specific SNP data formats not covered by the Writer class, implement a corresponding PHP class in this file.
• Implement classes and methods necessary to support the converted Python functionalities, ensuring they are compatible with the PHP 8.3 features and the overall architecture of the php-dna project.
• Include necessary PHP `use` statements to import any dependencies within the php-dna project or external PHP libraries.
• Document each class and method with PHPDoc comments, explaining their purpose and usage within the context of SNP data manipulation and file I/O operations.
• Ensure that the new PHP files follow the PSR-4 autoloading standard, allowing them to be easily integrated with the rest of the php-dna project.

• Running GitHub Actions for src/Snps/IO/AdditionalFile.php ✓ Edit

Check src/Snps/IO/AdditionalFile.php with contents:

Ran GitHub Actions for 199ae3bb01bfe22bad0a01e327cbb146b0d6db42:

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Step 3: 🔁 Code Review

I have finished reviewing the code for completeness. I did not find errors for sweep/write.

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