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+<?php
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+class FASTAImporter extends TripalImporter {
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+ /**
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+ * The name of this loader. This name will be presented to the site
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+ * user.
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+ */
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+ public static $name = 'Chado FASTA Loader';
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+
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+ /**
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+ * The machine name for this loader. This name will be used to construct
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+ * the URL for the loader.
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+ */
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+ public static $machine_name = 'fasta_loader';
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+
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+ /**
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+ * A brief description for this loader. This description will be
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+ * presented to the site user.
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+ */
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+ public static $description = 'Load sequences from a multi-FASTA file into Chado';
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+
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+ /**
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+ * An array containing the extensions of allowed file types.
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+ */
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+ public static $file_types = array('fasta');
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+
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+
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+ /**
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+ * Provides information to the user about the file upload. Typically this
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+ * may include a description of the file types allowed.
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+ */
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+ public static $upload_description = 'Please provide the FASTA file. The file must have a .fasta extension.';
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+
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+ /**
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+ * The title that should appear above the upload button.
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+ */
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+ public static $upload_title = 'FASTA Upload';
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+
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+
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+ public function form($form, &$form_state) {
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+
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+ // get the list of organisms
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+ $sql = "SELECT * FROM {organism} ORDER BY genus, species";
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+ $org_rset = chado_query($sql);
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+ $organisms = array();
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+ $organisms[''] = '';
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+ while ($organism = $org_rset->fetchObject()) {
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+ $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
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+ }
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+ $form['organism_id'] = array('#title' => t('Organism'),'#type' => t('select'),
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+ '#description' => t("Choose the organism to which these sequences are associated"),
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+ '#required' => TRUE,'#options' => $organisms
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+ );
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+
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+ // get the sequence ontology CV ID
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+ $values = array('name' => 'sequence');
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+ $cv = chado_select_record('cv', array('cv_id'), $values);
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+ $cv_id = $cv[0]->cv_id;
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+
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+ $form['seqtype'] = array('#type' => 'textfield','#title' => t('Sequence Type'),
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+ '#required' => TRUE,
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+ '#description' => t('Please enter the Sequence Ontology (SO) term name that describes the sequences in the FASTA file (e.g. gene, mRNA, polypeptide, etc...)'),
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+ '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/cvterm/$cv_id"
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+ );
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+
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+ $form['method'] = array('#type' => 'radios','#title' => 'Method','#required' => TRUE,
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+ '#options' => array(t('Insert only'),t('Update only'),t('Insert and update')
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+ ),
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+ '#description' => t('Select how features in the FASTA file are handled.
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+ Select "Insert only" to insert the new features. If a feature already
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+ exists with the same name or unique name and type then it is skipped.
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+ Select "Update only" to only update featues that already exist in the
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+ database. Select "Insert and Update" to insert features that do
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+ not exist and upate those that do.'),'#default_value' => 2
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+ );
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+ $form['match_type'] = array('#type' => 'radios','#title' => 'Name Match Type','#required' => TRUE,
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+ '#options' => array(t('Name'),t('Unique name')
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+ ),
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+ '#description' => t('Used for "updates only" or "insert and update" methods. Not required if method type is "insert".
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+ Feature data is stored in Chado with both a human-readable
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+ name and a unique name. If the features in your FASTA file are uniquely identified using
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+ a human-readable name then select the "Name" button. If your features are
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+ uniquely identified using the unique name then select the "Unique name" button. If you
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+ loaded your features first using the GFF loader then the unique name of each
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+ features were indicated by the "ID=" attribute and the name by the "Name=" attribute.
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+ By default, the FASTA loader will use the first word (character string
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+ before the first space) as the name for your feature. If
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+ this does not uniquely identify your feature consider specifying a regular expression in the advanced section below.
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+ Additionally, you may import both a name and a unique name for each sequence using the advanced options.'),
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+ '#default_value' => 1
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+ );
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+
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+ $form['analysis'] = array('#type' => 'fieldset','#title' => t('Analysis Used to Derive Features'),
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+ '#collapsed' => TRUE
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+ );
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+ $form['analysis']['desc'] = array(
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+ '#markup' => t("Why specify an analysis for a data load? All data comes
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+ from some place, even if downloaded from Genbank. By specifying
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+ analysis details for all data uploads, it allows an end user to reproduce the
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+ data set, but at least indicates the source of the data.")
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+ );
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+
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+ // get the list of organisms
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+ $sql = "SELECT * FROM {analysis} ORDER BY name";
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+ $org_rset = chado_query($sql);
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+ $analyses = array();
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+ $analyses[''] = '';
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+ while ($analysis = $org_rset->fetchObject()) {
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+ $analyses[$analysis->analysis_id] = "$analysis->name ($analysis->program $analysis->programversion, $analysis->sourcename)";
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+ }
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+ $form['analysis']['analysis_id'] = array('#title' => t('Analysis'),'#type' => t('select'),
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+ '#description' => t("Choose the analysis to which these features are associated"),
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+ '#required' => TRUE,'#options' => $analyses
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+ );
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+
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+ // Advanced Options
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+ $form['advanced'] = array('#type' => 'fieldset','#title' => t('Advanced Options'),
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+ '#collapsible' => TRUE,'#collapsed' => TRUE
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+ );
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+ $form['advanced']['re_help'] = array('#type' => 'item',
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+ '#value' => t('A regular expression is an advanced method for extracting information from a string of text.
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+ Your FASTA file may contain both a human-readable name and a unique name for each sequence.
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+ If you want to import
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+ both the name and unique name for all sequences, then you must provide regular expressions
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+ so that the loader knows how to separate them.
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+ Otherwise the name and uniquename will be the same.
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+ By default, this loader will use the first word in the definition
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+ lines of the FASTA file
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+ as the name or unique name of the feature.')
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+ );
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+ $form['advanced']['re_name'] = array('#type' => 'textfield',
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+ '#title' => t('Regular expression for the name'),'#required' => FALSE,
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+ '#description' => t('Enter the regular expression that will extract the
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+ feature name from the FASTA definition line. For example, for a
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+ defintion line with a name and unique name separated by a bar \'|\' (>seqname|uniquename),
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+ the regular expression for the name would be, "^(.*?)\|.*$". All FASTA
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+ definition lines begin with the ">" symbol. You do not need to incldue
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+ this symbol in your regular expression.')
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+ );
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+ $form['advanced']['re_uname'] = array('#type' => 'textfield',
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+ '#title' => t('Regular expression for the unique name'),'#required' => FALSE,
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+ '#description' => t('Enter the regular expression that will extract the
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+ feature name from the FASTA definition line. For example, for a
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+ defintion line with a name and unique name separated by a bar \'|\' (>seqname|uniquename),
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+ the regular expression for the unique name would be "^.*?\|(.*)$"). All FASTA
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+ definition lines begin with the ">" symbol. You do not need to incldue
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+ this symbol in your regular expression.')
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+ );
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+
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+ // Advanced database cross reference options.
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+ $form['advanced']['db'] = array('#type' => 'fieldset',
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+ '#title' => t('External Database Reference'),'#weight' => 6,'#collapsed' => TRUE
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+ );
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+ $form['advanced']['db']['re_accession'] = array('#type' => 'textfield',
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+ '#title' => t('Regular expression for the accession'),'#required' => FALSE,
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+ '#description' => t('Enter the regular expression that will extract the accession for the external database for each feature from the FASTA definition line.'),
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+ '#weight' => 2
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+ );
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+
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+ // get the list of databases
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+ $sql = "SELECT * FROM {db} ORDER BY name";
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+ $db_rset = chado_query($sql);
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+ $dbs = array();
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+ $dbs[''] = '';
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+ while ($db = $db_rset->fetchObject()) {
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+ $dbs[$db->db_id] = "$db->name";
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+ }
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+ $form['advanced']['db']['db_id'] = array('#title' => t('External Database'),
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+ '#type' => t('select'),
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+ '#description' => t("Plese choose an external database for which these sequences have a cross reference."),
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+ '#required' => FALSE,'#options' => $dbs,'#weight' => 1
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+ );
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+
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+ $form['advanced']['relationship'] = array('#type' => 'fieldset','#title' => t('Relationships'),
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+ '#weight' => 6,'#collapsed' => TRUE
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+ );
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+ $rels = array();
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+ $rels[''] = '';
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+ $rels['part_of'] = 'part of';
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+ $rels['derives_from'] = 'produced by (derives from)';
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+
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+ // Advanced references options
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+ $form['advanced']['relationship']['rel_type'] = array('#title' => t('Relationship Type'),
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+ '#type' => t('select'),
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+ '#description' => t("Use this option to create associations, or relationships between the
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+ features of this FASTA file and existing features in the database. For
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+ example, to associate a FASTA file of peptides to existing genes or transcript sequence,
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+ select the type 'produced by'. For a CDS sequences select the type 'part of'"),
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+ '#required' => FALSE,'#options' => $rels,'#weight' => 5
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+ );
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+ $form['advanced']['relationship']['re_subject'] = array('#type' => 'textfield',
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+ '#title' => t('Regular expression for the parent'),'#required' => FALSE,
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+ '#description' => t('Enter the regular expression that will extract the unique
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+ name needed to identify the existing sequence for which the
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+ relationship type selected above will apply.'),'#weight' => 6
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+ );
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+ $form['advanced']['relationship']['parent_type'] = array('#type' => 'textfield',
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+ '#title' => t('Parent Type'),'#required' => FALSE,
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+ '#description' => t('Please enter the Sequence Ontology term for the parent. For example
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+ if the FASTA file being loaded is a set of proteins that are
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+ products of genes, then use the SO term \'gene\' or \'transcript\' or equivalent. However,
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+ this type must match the type for already loaded features.'),
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+ '#weight' => 7
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+ );
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+ return $form;
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+ }
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+ /**
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+ * @see TripalImporter::formValidate()
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+ */
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+ public function formValidate($form, &$form_state) {
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+ $fasta_file = trim($form_state['values']['fasta_file']);
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+ $organism_id = $form_state['values']['organism_id'];
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+ $type = trim($form_state['values']['seqtype']);
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+ $method = trim($form_state['values']['method']);
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+ $match_type = trim($form_state['values']['match_type']);
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+ $re_name = trim($form_state['values']['re_name']);
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+ $re_uname = trim($form_state['values']['re_uname']);
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+ $re_accession = trim($form_state['values']['re_accession']);
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+ $db_id = $form_state['values']['db_id'];
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+ $rel_type = $form_state['values']['rel_type'];
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+ $re_subject = trim($form_state['values']['re_subject']);
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+ $parent_type = trim($form_state['values']['parent_type']);
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+
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+ if ($method == 0) {
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+ $method = 'Insert only';
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+ }
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+ if ($method == 1) {
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+ $method = 'Update only';
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+ }
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+ if ($method == 2) {
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+ $method = 'Insert and update';
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+ }
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+
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+ if ($match_type == 0) {
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+ $match_type = 'Name';
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+ }
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+
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+ if ($match_type == 1) {
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+ $match_type = 'Unique name';
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+ }
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+
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+ if ($re_name and !$re_uname and strcmp($match_type, 'Unique name') == 0) {
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+ form_set_error('re_uname', t("You must provide a regular expression to identify the sequence unique name"));
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+ }
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+
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+ if (!$re_name and $re_uname and strcmp($match_type, 'Name') == 0) {
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+ form_set_error('re_name', t("You must provide a regular expression to identify the sequence name"));
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+ }
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+
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+ // check to see if the file is located local to Drupal
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+ $fasta_file = trim($fasta_file);
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+ $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $fasta_file;
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+ if (!file_exists($dfile)) {
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+ // if not local to Drupal, the file must be someplace else, just use
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+ // the full path provided
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+ $dfile = $fasta_file;
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+ }
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+ if (!file_exists($dfile)) {
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+ form_set_error('fasta_file', t("Cannot find the file on the system. Check that the file exists or that the web server has permissions to read the file."));
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+ }
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+
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+ // make sure if a relationship is specified that all fields are provided.
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+ if (($rel_type or $parent_type) and !$re_subject) {
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+ form_set_error('re_subject', t("Please provide a regular expression for the parent"));
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+ }
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+ if (($rel_type or $re_subject) and !$parent_type) {
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+ form_set_error('parent_type', t("Please provide a SO term for the parent"));
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+ }
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+ if (($parent_type or $re_subject) and !$rel_type) {
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+ form_set_error('rel_type', t("Please select a relationship type"));
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+ }
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+
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+ // make sure if a database is specified that all fields are provided
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+ if ($db_id and !$re_accession) {
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+ form_set_error('re_accession', t("Please provide a regular expression for the accession"));
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+ }
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+ if ($re_accession and !$db_id) {
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+ form_set_error('db_id', t("Please select a database"));
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+ }
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+
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+ // check to make sure the types exists
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+ $cvtermsql ="
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+ SELECT CVT.cvterm_id
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+ FROM {cvterm} CVT
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+ INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
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+ LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
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+ WHERE cv.name = :cvname and (CVT.name = :name or CVTS.synonym = :synonym)
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+ ";
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+ $cvterm = chado_query($cvtermsql,
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+ array(':cvname' => 'sequence',':name' => $type,':synonym' => $type))->fetchObject();
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+ if (!$cvterm) {
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+ form_set_error('type', t("The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."));
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+ }
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+ if ($rel_type) {
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+ $cvterm = chado_query($cvtermsql, array(':cvname' => 'sequence',':name' => $parent_type,
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+ ':synonym' => $parent_type
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+ ))->fetchObject();
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+ if (!$cvterm) {
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+ form_set_error('parent_type', t("The Sequence Ontology (SO) term selected for the parent relationship is not available in the database. Please check spelling or select another."));
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+ }
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+ }
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+
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+ // check to make sure the 'relationship' and 'sequence' ontologies are loaded
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+ $form_state['storage']['dfile'] = $dfile;
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+ }
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+ /**
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+ * @see TripalImporter::run()
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+ */
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+ public function run($details, $job_id = NULL) {
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+ $arguments = $details->arguments;
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+
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+ $dfile = $arguments['file_path'];
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+ $organism_id = $arguments['organism_id'];
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+ $type = $arguments['seqtype'];
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+ $method = $arguments['method'];
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+ $match_type = $arguments['match_type'];
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+ $re_name = $arguments['re_name'];
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+ $re_uname = $arguments['re_uname'];
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+ $re_accession = $arguments['re_accession'];
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+ $db_id = $arguments['db_id'];
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+ $rel_type = $arguments['rel_type'];
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+ $re_subject = $arguments['re_subject'];
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+ $parent_type = $arguments['parent_type'];
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+ $analysis_id = $arguments['analysis_id'];
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+
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+ $this->load($dfile, $organism_id, $type, $re_name, $re_uname, $re_accession,
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+ $db_id, $rel_type, $re_subject, $parent_type, $method, $uid, $analysis_id,
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+ $match_type, $job_id);
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+ }
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+ /**
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+ * Load a fasta file.
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+ *
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+ * @param $dfile
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+ * The full path to the fasta file to load.
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+ * @param $organism_id
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+ * The organism_id of the organism these features are from.
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+ * @param $type
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+ * The type of features contained in the fasta file.
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+ * @param $re_name
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+ * The regular expression to extract the feature.name from the fasta header.
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+ * @param $re_uname
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+ * The regular expression to extract the feature.uniquename from the fasta
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+ * header.
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+ * @param $re_accession
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+ * The regular expression to extract the accession of the feature.dbxref_id.
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+ * @param $db_id
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+ * The database ID of the above accession.
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+ * @param $rel_type
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+ * The type of relationship when creating a feature_relationship between
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+ * this feature (object) and an extracted subject.
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+ * @param $re_subject
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+ * The regular expression to extract the uniquename of the feature to be
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+ * the subject of the above specified relationship.
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+ * @param $parent_type
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|
|
+ * The type of the parent feature.
|
|
|
+ * @param $method
|
|
|
+ * The method of feature adding. (ie: 'Insert only', 'Update only',
|
|
|
+ * 'Insert and update').
|
|
|
+ * @param $uid
|
|
|
+ * The user id of the user who submitted the job.
|
|
|
+ * @param $analysis_id
|
|
|
+ * The analysis_id to associate the features in this fasta file with.
|
|
|
+ * @param $match_type
|
|
|
+ * Whether to match existing features based on the 'Name' or 'Unique name'.
|
|
|
+ * @param $job
|
|
|
+ * The tripal job
|
|
|
+ */
|
|
|
+ private function loadFasta($dfile, $organism_id, $type, $re_name, $re_uname, $re_accession,
|
|
|
+ $db_id, $rel_type, $re_subject, $parent_type, $method, $uid, $analysis_id, $match_type,
|
|
|
+ $job = NULL) {
|
|
|
+
|
|
|
+ // First get the type for this sequence.
|
|
|
+ $cvtermsql = "
|
|
|
+ SELECT CVT.cvterm_id
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
|
|
|
+ LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
|
|
|
+ WHERE cv.name = :cvname and (CVT.name = :name or CVTS.synonym = :synonym)
|
|
|
+ ";
|
|
|
+ $cvterm = chado_query($cvtermsql, array(':cvname' => 'sequence',':name' => $type,':synonym' => $type))->fetchObject();
|
|
|
+ if (!$cvterm) {
|
|
|
+ tripal_report_error("T_fasta_loader", TRIPAL_ERROR,
|
|
|
+ "Cannot find the term type: '%type'", array('%type' => $type));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Second, if there is a parent type then get that.
|
|
|
+ if ($parent_type) {
|
|
|
+ $parentcvterm = chado_query($cvtermsql, array(':cvname' => 'sequence', ':name' => $parent_type,':synonym' => $parent_type))->fetchObject();
|
|
|
+ if (!$parentcvterm) {
|
|
|
+ tripal_report_error("T_fasta_loader", TRIPAL_ERROR, "Cannot find the paretne term type: '%type'", array(
|
|
|
+ '%type' => $parentcvterm
|
|
|
+ ));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Third, if there is a relationship type then get that.
|
|
|
+ if ($rel_type) {
|
|
|
+ $relcvterm = chado_query($cvtermsql, array(':cvname' => 'sequence',':name' => $rel_type,':synonym' => $rel_type))->fetchObject();
|
|
|
+ if (!$relcvterm) {
|
|
|
+ tripal_report_error("T_fasta_loader", TRIPAL_ERROR, "Cannot find the relationship term type: '%type'", array(
|
|
|
+ '%type' => $relcvterm
|
|
|
+ ));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // We need to get the table schema to make sure we don't overrun the
|
|
|
+ // size of fields with what our regular expressions retrieve
|
|
|
+ $feature_tbl = chado_get_schema('feature');
|
|
|
+ $dbxref_tbl = chado_get_schema('dbxref');
|
|
|
+
|
|
|
+ print "Step 1: finding sequences\n";
|
|
|
+ $filesize = filesize($dfile);
|
|
|
+ $fh = fopen($dfile, 'r');
|
|
|
+ if (!$fh) {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "cannot open file: %dfile", array(
|
|
|
+ '%dfile' => $dfile
|
|
|
+ ));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Calculate the interval at which we will print to the screen that status.
|
|
|
+ $interval = intval($filesize * 0.01);
|
|
|
+ if ($interval < 1) {
|
|
|
+ $interval = 1;
|
|
|
+ }
|
|
|
+ $inv_read = 0;
|
|
|
+ $num_read = 0;
|
|
|
+
|
|
|
+ // Iterate through the lines of the file. Keep a record for
|
|
|
+ // where in the file each line is at for later import.
|
|
|
+ $seqs = array();
|
|
|
+ $num_seqs = 0;
|
|
|
+ $prev_pos = 0;
|
|
|
+ $set_start = FALSE;
|
|
|
+ while ($line = fgets($fh)) {
|
|
|
+ $num_read += strlen($line);
|
|
|
+ $intv_read += strlen($line);
|
|
|
+
|
|
|
+ // If we encounter a definition line then get the name, uniquename,
|
|
|
+ // accession and relationship subject from the definition line.
|
|
|
+ if (preg_match('/^>/', $line)) {
|
|
|
+
|
|
|
+ // Remove the > symbol from the defline.
|
|
|
+ $defline = preg_replace("/^>/", '', $line);
|
|
|
+
|
|
|
+ // Get the feature name if a regular expression is provided.
|
|
|
+ if ($re_name) {
|
|
|
+ if (!preg_match("/$re_name/", $defline, $matches)) {
|
|
|
+ tripal_report_error('trp-fasta', "ERROR: Regular expression for the feature name finds nothing. Line %line.", array(
|
|
|
+ '%line' => $i
|
|
|
+ ), 'error');
|
|
|
+ }
|
|
|
+ elseif (strlen($matches[1]) > $feature_tbl['fields']['name']['length']) {
|
|
|
+ tripal_report_error('trp-fasta', "WARNING: Regular expression retrieves a value too long for the feature name. Line %line.", array(
|
|
|
+ '%line' => $i
|
|
|
+ ), 'error');
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $name = trim($matches[1]);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // If the match_type is name and no regular expression was provided
|
|
|
+ // then use the first word as the name, otherwise we don't set the name.
|
|
|
+ elseif (strcmp($match_type, 'Name') == 0) {
|
|
|
+ if (preg_match("/^\s*(.*?)[\s\|].*$/", $defline, $matches)) {
|
|
|
+ if (strlen($matches[1]) > $feature_tbl['fields']['name']['length']) {
|
|
|
+ tripal_report_error('trp-fasta', "WARNING: Regular expression retrieves a feature name too long for the feature name. Line %line.", array(
|
|
|
+ '%line' => $i), 'error');
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $name = trim($matches[1]);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ tripal_report_error('trp-fasta', "ERROR: Cannot find a feature name. Line %line.", array(
|
|
|
+ '%line' => $i), 'error');
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Get the feature uniquename if a regular expression is provided.
|
|
|
+ if ($re_uname) {
|
|
|
+ if (!preg_match("/$re_uname/", $defline, $matches)) {
|
|
|
+ tripal_report_error('trp-fasta', "ERROR: Regular expression for the feature unique name finds nothing. Line %line.", array(
|
|
|
+ '%line' => $i), 'error');
|
|
|
+ }
|
|
|
+ $uname = trim($matches[1]);
|
|
|
+ }
|
|
|
+ // If the match_type is name and no regular expression was provided
|
|
|
+ // then use the first word as the name, otherwise, we don't set the
|
|
|
+ // unqiuename.
|
|
|
+ elseif (strcmp($match_type, 'Unique name') == 0) {
|
|
|
+ if (preg_match("/^\s*(.*?)[\s\|].*$/", $defline, $matches)) {
|
|
|
+ $uname = trim($matches[1]);
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ tripal_report_error('trp-fasta', "ERROR: Cannot find a feature unique name. Line %line.", array(
|
|
|
+ '%line' => $i), 'error');
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Get the accession if a regular expression is provided.
|
|
|
+ preg_match("/$re_accession/", $defline, $matches);
|
|
|
+ if (strlen($matches[1]) > $dbxref_tbl['fields']['accession']['length']) {
|
|
|
+ tripal_report_error('trp-fasta', "WARNING: Regular expression retrieves an accession too long for the feature name. " .
|
|
|
+ "Cannot add cross reference. Line %line.", array('%line' => $i
|
|
|
+ ), 'warning');
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $accession = trim($matches[1]);
|
|
|
+ }
|
|
|
+
|
|
|
+ // Get the relationship subject
|
|
|
+ preg_match("/$re_subject/", $line, $matches);
|
|
|
+ $subject = trim($matches[1]);
|
|
|
+
|
|
|
+ // Add the details to the sequence.
|
|
|
+ $seqs[$num_seqs] = array(
|
|
|
+ 'name' => $name,
|
|
|
+ 'uname' => $uname,
|
|
|
+ 'accession' => $accession,
|
|
|
+ 'subject' => $subject,
|
|
|
+ 'seq_start' => ftell($fh)
|
|
|
+ );
|
|
|
+ $set_start = TRUE;
|
|
|
+ // If this isn't the first sequence, then we want to specify where
|
|
|
+ // the previous sequence ended.
|
|
|
+ if ($num_seqs > 0) {
|
|
|
+ $seqs[$num_seqs - 1]['seq_end'] = $prev_pos;
|
|
|
+ }
|
|
|
+ $num_seqs++;
|
|
|
+ }
|
|
|
+ // Keep the current file position so we can use it to set the sequence
|
|
|
+ // ending position
|
|
|
+ $prev_pos = ftell($fh);
|
|
|
+
|
|
|
+ // update the job status every % bytes
|
|
|
+ if ($job and $intv_read >= $interval) {
|
|
|
+ $intv_read = 0;
|
|
|
+ $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
|
|
|
+ if ($name) {
|
|
|
+ print "Parsing Line $i (" . $percent . "%). Memory: " . number_format(memory_get_usage()) .
|
|
|
+ " bytes.\r";
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ print "Parsing Line $i (" . $percent . "%). Memory: " . number_format(memory_get_usage()) .
|
|
|
+ " bytes.\r";
|
|
|
+ }
|
|
|
+ tripal_set_job_progress($job, intval(($num_read / $filesize) * 100));
|
|
|
+ }
|
|
|
+ }
|
|
|
+ $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
|
|
|
+ print "Parsing Line $i (" . $percent . "%). Memory: " . number_format(memory_get_usage()) .
|
|
|
+ " bytes.\r";
|
|
|
+ tripal_set_job_progress($job, 50);
|
|
|
+
|
|
|
+ // Set the end position for the last sequence.
|
|
|
+ $seqs[$num_seqs - 1]['seq_end'] = $num_read - strlen($line);
|
|
|
+
|
|
|
+ // Now that we know where the sequences are in the file we need to add them.
|
|
|
+ print "\nStep 2: Importing sequences\n";
|
|
|
+ for ($i = 0; $i < $num_seqs; $i++) {
|
|
|
+ $seq = $seqs[$i];
|
|
|
+ print "Importing " . ($i + 1) . " of $num_seqs. ";
|
|
|
+ if ($name) {
|
|
|
+ print "Current feature: " . $seq['name'] . ".\n";
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ print "Current feature: " . $seq['uname'] . ".\n";
|
|
|
+ }
|
|
|
+
|
|
|
+ loadFastaFeature($fh, $seq['name'], $seq['uname'], $db_id, $seq['accession'], $seq['subject'], $rel_type, $parent_type, $analysis_id, $organism_id, $cvterm, $source, $method, $re_name, $match_type, $parentcvterm, $relcvterm, $seq['seq_start'], $seq['seq_end']);
|
|
|
+ }
|
|
|
+ tripal_set_job_progress($job, 100);
|
|
|
+ fclose($fh);
|
|
|
+
|
|
|
+ }
|
|
|
+
|
|
|
+ /**
|
|
|
+ * A helper function for loadFasta() to load a single feature
|
|
|
+ *
|
|
|
+ * @ingroup fasta_loader
|
|
|
+ */
|
|
|
+ private function loadFastaFeature($fh, $name, $uname, $db_id, $accession, $parent,
|
|
|
+ $rel_type, $parent_type, $analysis_id, $organism_id, $cvterm, $source, $method, $re_name,
|
|
|
+ $match_type, $parentcvterm, $relcvterm, $seq_start, $seq_end) {
|
|
|
+
|
|
|
+ // Check to see if this feature already exists if the match_type is 'Name'.
|
|
|
+ if (strcmp($match_type, 'Name') == 0) {
|
|
|
+ $values = array('organism_id' => $organism_id,'name' => $name,'type_id' => $cvterm->cvterm_id
|
|
|
+ );
|
|
|
+ $results = chado_select_record('feature', array('feature_id'
|
|
|
+ ), $values);
|
|
|
+ if (count($results) > 1) {
|
|
|
+ tripal_report_error('T_fasta_loader', "Multiple features exist with the name '%name' of type
|
|
|
+ '%type' for the organism. skipping", array('%name' => $name,'%type' => $type));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ if (count($results) == 1) {
|
|
|
+ $feature = $results[0];
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Check if this feature already exists if the match_type is 'Unique Name'.
|
|
|
+ if (strcmp($match_type, 'Unique name') == 0) {
|
|
|
+ $values = array(
|
|
|
+ 'organism_id' => $organism_id,
|
|
|
+ 'uniquename' => $uname,
|
|
|
+ 'type_id' => $cvterm->cvterm_id
|
|
|
+ );
|
|
|
+
|
|
|
+ $results = chado_select_record('feature', array('feature_id'), $values);
|
|
|
+ if (count($results) > 1) {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_WARNING, "Multiple features exist with the name '%name' of type '%type' for the organism. skipping", array(
|
|
|
+ '%name' => $name,'%type' => $type));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ if (count($results) == 1) {
|
|
|
+ $feature = $results[0];
|
|
|
+ }
|
|
|
+
|
|
|
+ // If the feature exists but this is an "insert only" then skip.
|
|
|
+ if ($feature and (strcmp($method, 'Insert only') == 0)) {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_WARNING, "Feature already exists '%name' ('%uname') while matching on %type. Skipping insert.", array(
|
|
|
+ '%name' => $name,'%uname' => $uname,'%type' => drupal_strtolower($match_type)
|
|
|
+ ));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // If we don't have a feature and we're doing an insert then do the insert.
|
|
|
+ $inserted = 0;
|
|
|
+ if (!$feature and (strcmp($method, 'Insert only') == 0 or strcmp($method, 'Insert and update') == 0)) {
|
|
|
+ // If we have a unique name but not a name then set them to be the same
|
|
|
+ if (!$uname) {
|
|
|
+ $uname = $name;
|
|
|
+ }
|
|
|
+ elseif (!$name) {
|
|
|
+ $name = $uname;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Insert the feature record.
|
|
|
+ $values = array(
|
|
|
+ 'organism_id' => $organism_id,
|
|
|
+ 'name' => $name,
|
|
|
+ 'uniquename' => $uname,
|
|
|
+ 'type_id' => $cvterm->cvterm_id
|
|
|
+ );
|
|
|
+ $success = chado_insert_record('feature', $values);
|
|
|
+ if (!$success) {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to insert feature '%name (%uname)'", array(
|
|
|
+ '%name' => $name,'%uname' => $numane));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ // now get the feature we just inserted
|
|
|
+ $values = array(
|
|
|
+ 'organism_id' => $organism_id,
|
|
|
+ 'uniquename' => $uname,
|
|
|
+ 'type_id' => $cvterm->cvterm_id
|
|
|
+ );
|
|
|
+ $results = chado_select_record('feature', array('feature_id'), $values);
|
|
|
+ if (count($results) == 1) {
|
|
|
+ $inserted = 1;
|
|
|
+ $feature = $results[0];
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to retreive newly inserted feature '%name (%uname)'", array(
|
|
|
+ '%name' => $name,'%uname' => $numane));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Add the residues for this feature
|
|
|
+ loadFastaResidues($fh, $feature->feature_id, $seq_start, $seq_end);
|
|
|
+ }
|
|
|
+
|
|
|
+ // if we don't have a feature and the user wants to do an update then fail
|
|
|
+ if (!$feature and (strcmp($method, 'Update only') == 0 or
|
|
|
+ drupal_strcmp($method, 'Insert and update') == 0)) {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to find feature '%name' ('%uname') while matching on " .
|
|
|
+ drupal_strtolower($match_type), array('%name' => $name,'%uname' => $uname));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ // if we do have a feature and this is an update then proceed with the update
|
|
|
+ if ($feature and !$inserted and (strcmp($method, 'Update only') == 0 or
|
|
|
+ strcmp($method, 'Insert and update') == 0)) {
|
|
|
+
|
|
|
+ // if the user wants to match on the Name field
|
|
|
+ if (strcmp($match_type, 'Name') == 0) {
|
|
|
+
|
|
|
+ // if we're matching on the name but do not have a unique name then we
|
|
|
+ // don't want to update the uniquename.
|
|
|
+ $values = array();
|
|
|
+ if ($uname) {
|
|
|
+
|
|
|
+ // First check to make sure that by changing the unique name of this
|
|
|
+ // feature that we won't conflict with another existing feature of
|
|
|
+ // the same name
|
|
|
+ $values = array(
|
|
|
+ 'organism_id' => $organism_id,
|
|
|
+ 'uniquename' => $uname,
|
|
|
+ 'type_id' => $cvterm->cvterm_id
|
|
|
+ );
|
|
|
+ $results = chado_select_record('feature', array('feature_id'
|
|
|
+ ), $values);
|
|
|
+ if (count($results) > 0) {
|
|
|
+ tripal_report_error('T_fasta_loader', "Cannot update the feature '%name' with a uniquename of '%uname' and type of '%type' as it
|
|
|
+ conflicts with an existing feature with the same uniquename and type.", array(
|
|
|
+ '%name' => $name,'%uname' => $uname,'%type' => $type
|
|
|
+ ));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ // the changes to the uniquename don't conflict so proceed with the update
|
|
|
+ $values = array('uniquename' => $uname);
|
|
|
+ $match = array(
|
|
|
+ 'name' => $name,
|
|
|
+ 'organism_id' => $organism_id,
|
|
|
+ 'type_id' => $cvterm->cvterm_id
|
|
|
+ );
|
|
|
+
|
|
|
+ // perform the update
|
|
|
+ $success = chado_update_record('feature', $match, $values);
|
|
|
+ if (!$success) {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to update feature '%name' ('%name')", array(
|
|
|
+ '%name' => $name,'%uiname' => $uname
|
|
|
+ ));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // If the user wants to match on the unique name field.
|
|
|
+ if (strcmp($match_type, 'Unique name') == 0) {
|
|
|
+ // If we're matching on the uniquename and have a new name then
|
|
|
+ // we want to update the name.
|
|
|
+ $values = array();
|
|
|
+ if ($name) {
|
|
|
+ $values = array('name' => $name);
|
|
|
+ $match = array(
|
|
|
+ 'uniquename' => $uname,
|
|
|
+ 'organism_id' => $organism_id,
|
|
|
+ 'type_id' => $cvterm->cvterm_id
|
|
|
+ );
|
|
|
+ $success = chado_update_record('feature', $match, $values);
|
|
|
+ if (!$success) {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to update feature '%name' ('%name')", array(
|
|
|
+ '%name' => $name,'%uiname' => $uname
|
|
|
+ ));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Update the residues for this feature
|
|
|
+ loadFastaResidues($fh, $feature->feature_id, $seq_start, $seq_end);
|
|
|
+
|
|
|
+ // add in the analysis link
|
|
|
+ if ($analysis_id) {
|
|
|
+ // if the association doens't alredy exist then add one
|
|
|
+ $values = array(
|
|
|
+ 'analysis_id' => $analysis_id,
|
|
|
+ 'feature_id' => $feature->feature_id
|
|
|
+ );
|
|
|
+ $results = chado_select_record('analysisfeature', array('analysisfeature_id'), $values);
|
|
|
+ if (count($results) == 0) {
|
|
|
+ $success = chado_insert_record('analysisfeature', $values);
|
|
|
+ if (!$success) {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to associate analysis and feature '%name' ('%name')", array(
|
|
|
+ '%name' => $name,'%uname' => $uname
|
|
|
+ ));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // now add the database cross reference
|
|
|
+ if ($db_id) {
|
|
|
+ // check to see if this accession reference exists, if not add it
|
|
|
+ $values = array(
|
|
|
+ 'db_id' => $db_id,
|
|
|
+ 'accession' => $accession
|
|
|
+ );
|
|
|
+ $results = chado_select_record('dbxref', array('dbxref_id'), $values);
|
|
|
+ // if the accession doesn't exist then add it
|
|
|
+ if (count($results) == 0) {
|
|
|
+ $results = chado_insert_record('dbxref', $values);
|
|
|
+ if (!$results) {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to add database accession '%accession'", array(
|
|
|
+ '%accession' => $accession));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ $results = chado_select_record('dbxref', array('dbxref_id'), $values);
|
|
|
+ if (count($results) == 1) {
|
|
|
+ $dbxref = $results[0];
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to retreive newly inserted dbxref '%name (%uname)'", array(
|
|
|
+ '%name' => $name,'%uname' => $numane));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $dbxref = $results[0];
|
|
|
+ }
|
|
|
+
|
|
|
+ // check to see if the feature dbxref record exists if not, then add it
|
|
|
+ $values = array(
|
|
|
+ 'feature_id' => $feature->feature_id,
|
|
|
+ 'dbxref_id' => $dbxref->dbxref_id
|
|
|
+ );
|
|
|
+ $results = chado_select_record('feature_dbxref', array('feature_dbxref_id'), $values);
|
|
|
+ if (count($results) == 0) {
|
|
|
+ $success = chado_insert_record('feature_dbxref', $values);
|
|
|
+ if (!$success) {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to add associate database accession '%accession' with feature", array(
|
|
|
+ '%accession' => $accession
|
|
|
+ ));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // now add in the relationship if one exists. If not, then add it
|
|
|
+ if ($rel_type) {
|
|
|
+ $values = array('organism_id' => $organism_id,'uniquename' => $parent,
|
|
|
+ 'type_id' => $parentcvterm->cvterm_id
|
|
|
+ );
|
|
|
+ $results = chado_select_record('feature', array('feature_id'
|
|
|
+ ), $values);
|
|
|
+ if (count($results) != 1) {
|
|
|
+ tripal_report_error('T_fasta_loader', "Cannot find a unique fature for the parent '%parent' of type
|
|
|
+ '%type' for the feature.", array(
|
|
|
+ '%parent' => $parent,'%type' => $parent_type
|
|
|
+ ));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ $parent_feature = $results[0];
|
|
|
+
|
|
|
+ // check to see if the relationship already exists if not then add it
|
|
|
+ $values = array(
|
|
|
+ 'subject_id' => $feature->feature_id,
|
|
|
+ 'object_id' => $parent_feature->feature_id,
|
|
|
+ 'type_id' => $relcvterm->cvterm_id
|
|
|
+ );
|
|
|
+ $results = chado_select_record('feature_relationship', array('feature_relationship_id'), $values);
|
|
|
+ if (count($results) == 0) {
|
|
|
+ $success = chado_insert_record('feature_relationship', $values);
|
|
|
+ if (!$success) {
|
|
|
+ tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to add associate database accession '%accession' with feature", array(
|
|
|
+ '%accession' => $accession
|
|
|
+ ));
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+ /**
|
|
|
+ * Adds the residues column to the feature.
|
|
|
+ *
|
|
|
+ * This function seeks to the proper location in the file for the sequence
|
|
|
+ * and reads in chunks of sequence and appends them to the feature.residues
|
|
|
+ * column in the database.
|
|
|
+ *
|
|
|
+ * @param $fh
|
|
|
+ * @param $feature_id
|
|
|
+ * @param $seq_start
|
|
|
+ * @param $seq_end
|
|
|
+ */
|
|
|
+ private function loadFastaResidues($fh, $feature_id, $seq_start, $seq_end) {
|
|
|
+
|
|
|
+ // First position the file at the beginning of the sequence
|
|
|
+ fseek($fh, $seq_start, SEEK_SET);
|
|
|
+ $chunk_size = 100000000;
|
|
|
+ $chunk = '';
|
|
|
+ $seqlen = ($seq_end - $seq_start) + 1;
|
|
|
+
|
|
|
+ // Calculate the interval at which we updated the precent complete.
|
|
|
+ $interval = intval($seqlen * 0.01);
|
|
|
+ if ($interval < 1) {
|
|
|
+ $interval = 1;
|
|
|
+ }
|
|
|
+ // We don't to repeat the update too often or it slows things down, so
|
|
|
+ // if the interval is less than 1000 then bring it up to that.
|
|
|
+ if ($interval < 100000) {
|
|
|
+ $interval = 100000;
|
|
|
+ }
|
|
|
+ $chunk_intv_read = 0;
|
|
|
+ $intv_read = 0;
|
|
|
+ $num_read = 0;
|
|
|
+ $total_seq_size = 0;
|
|
|
+
|
|
|
+ // First, make sure we don't have a null in the residues
|
|
|
+ $sql = "UPDATE {feature} SET residues = '' WHERE feature_id = :feature_id";
|
|
|
+ chado_query($sql, array(':feature_id' => $feature_id
|
|
|
+ ));
|
|
|
+
|
|
|
+ // Read in the lines until we reach the end of the sequence. Once we
|
|
|
+ // get a specific bytes read then append the sequence to the one in the
|
|
|
+ // database.
|
|
|
+ print "Sequence complete: 0%. Memory: " . number_format(memory_get_usage()) . " bytes. \r";
|
|
|
+ while ($line = fgets($fh)) {
|
|
|
+ $num_read += strlen($line) + 1;
|
|
|
+ $chunk_intv_read += strlen($line) + 1;
|
|
|
+ $intv_read += strlen($line) + 1;
|
|
|
+ $chunk .= trim($line);
|
|
|
+
|
|
|
+ // If we've read in enough of the sequence then append it to the database.
|
|
|
+ if ($chunk_intv_read >= $chunk_size) {
|
|
|
+ $sql = "
|
|
|
+ UPDATE {feature}
|
|
|
+ SET residues = residues || :chunk
|
|
|
+ WHERE feature_id = :feature_id
|
|
|
+ ";
|
|
|
+ $success = chado_query($sql, array(':feature_id' => $feature_id,':chunk' => $chunk
|
|
|
+ ));
|
|
|
+ if (!$success) {
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ $total_seq_size += strlen($chunk);
|
|
|
+ $chunk = '';
|
|
|
+ $chunk_intv_read = 0;
|
|
|
+ }
|
|
|
+ if ($intv_read >= $interval) {
|
|
|
+ $percent = sprintf("%.2f", ($total_seq_size / $seqlen) * 100);
|
|
|
+ print "Sequence complete: " . $percent . "%. Memory: " . number_format(memory_get_usage()) .
|
|
|
+ " bytes. \r";
|
|
|
+ $intv_read = 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ // If we've reached the ned of the sequence then break out of the loop
|
|
|
+ if (ftell($fh) == $seq_end) {
|
|
|
+ break;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // write the last bit of sequence if it remains
|
|
|
+ if (strlen($chunk) > 0) {
|
|
|
+ $sql = "
|
|
|
+ UPDATE {feature}
|
|
|
+ SET residues = residues || :chunk
|
|
|
+ WHERE feature_id = :feature_id
|
|
|
+ ";
|
|
|
+ $success = chado_query($sql, array(':feature_id' => $feature_id,':chunk' => $chunk
|
|
|
+ ));
|
|
|
+ if (!$success) {
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ $total_seq_size += strlen($chunk);
|
|
|
+ $chunk = '';
|
|
|
+ $chunk_intv_read = 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Now update the seqlen and md5checksum fields
|
|
|
+ $sql = "UPDATE {feature} SET seqlen = char_length(residues), md5checksum = md5(residues) WHERE feature_id = :feature_id";
|
|
|
+ chado_query($sql, array(':feature_id' => $feature_id
|
|
|
+ ));
|
|
|
+
|
|
|
+ $percent = sprintf("%.2f", ($num_read / $seqlen) * 100);
|
|
|
+ print "Sequence complete: " . $percent . "%. Memory: " . number_format(memory_get_usage()) .
|
|
|
+ " bytes. \r";
|
|
|
+ }
|
|
|
+
|
|
|
+}
|
Stephen Ficklin