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Tripal v1.0 (6.x-1.0)
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Tripal v1.0 (6.x-1.0)
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Go to the source code of this file.
Functions | |
| tripal_feature_gff3_load_form () | |
| tripal_feature_gff3_load_form_validate ($form, &$form_state) | |
| tripal_feature_gff3_load_form_submit ($form, &$form_state) | |
| tripal_feature_load_gff3 ($gff_file, $organism_id, $analysis_id, $add_only=0, $update=0, $refresh=0, $remove=0, $use_transaction=1, $target_organism_id=NULL, $target_type=NULL, $create_target=0, $start_line=1, $landmark_type= '', $alt_id_attr= '', $job=NULL) | |
| tripal_feature_load_gff3_derives_from ($feature, $subject, $organism) | |
| tripal_feature_load_gff3_parents ($feature, $cvterm, $parents, $organism_id, $fmin) | |
| tripal_feature_load_gff3_dbxref ($feature, $dbxrefs) | |
| tripal_feature_load_gff3_ontology ($feature, $dbxrefs) | |
| tripal_feature_load_gff3_alias ($feature, $aliases) | |
| tripal_feature_load_gff3_feature ($organism, $analysis_id, $cvterm, $uniquename, $name, $residues, $is_analysis= 'f', $is_obsolete= 'f', $add_only, $score) | |
| tripal_feature_load_gff3_featureloc ($feature, $organism, $landmark, $fmin, $fmax, $strand, $phase, $is_fmin_partial, $is_fmax_partial, $residue_info, $locgroup, $landmark_type_id= '', $landmark_organism_id= '', $create_landmark=0, $landmark_is_target=0) | |
| tripal_feature_load_gff3_property ($feature, $property, $value) | |
| tripal_feature_load_gff3_fasta ($fh, $interval, &$num_read, &$intv_read, &$line_num) | |
| tripal_feature_load_gff3_target ($feature, $tags, $target_organism_id, $target_type, $create_target, $attr_locgroup) | |
Definition in file gff_loader.inc.
| tripal_feature_load_gff3_fasta | ( | $ | fh, |
| $ | interval, | ||
| &$ | num_read, | ||
| &$ | intv_read, | ||
| &$ | line_num | ||
| ) |
Definition at line 1718 of file gff_loader.inc.
{
print "Loading FASTA sequences\n";
$residues = '';
$sql = "
PREPARE sel_gfftemp_un (text) AS
SELECT feature_id FROM tripal_gff_temp
WHERE uniquename = $1
";
$status = tripal_core_chado_prepare('sel_gfftemp_un', $sql, array('text'));
if (!$status) {
watchdog('T_gff3_loader', 'Cannot prepare statement \'sel_gfftemp_un\'.',
array(), WATCHDOG_ERROR);
return '';
}
$id = NULL;
// iterate through the remaining lines of the file
while ($line = fgets($fh)) {
$line_num++;
$size = drupal_strlen($line);
$num_read += $size;
$intv_read += $size;
$line = trim($line);
// update the job status every 1% features
if ($job and $intv_read >= $interval) {
$intv_read = 0;
$percent = sprintf("%.2f", ($num_read / $filesize) * 100);
print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
tripal_job_set_progress($job, intval(($num_read / $filesize) * 100));
}
// if we encounter a definition line then get the name, uniquename,
// accession and relationship subject from the definition line
if (preg_match('/^>/', $line)) {
// if we are beginning a new sequence then save the last one we
// just finished.
if ($id) {
$sql = "EXECUTE sel_gfftemp_un('%s')";
$result = tripal_core_chado_execute_prepared('sel_gfftemp_un', $sql, array($id));
if (!$result) {
watchdog('T_gff3_loader', 'Cannot find feature to assign FASTA sequence: %uname',
array('%uname' => $id), WATCHDOG_WARNING);
}
// if we have a feature then add the residues
else {
$feature = db_fetch_object($result);
$values = array('residues' => $residues);
$match = array('feature_id' => $feature->feature_id);
$options = array('statement_name' => 'upd_feature_re');
tripal_core_chado_update('feature', $match, $values, $options);
}
}
// get the feature ID for this ID from the tripal_gff_temp table
$id = preg_replace('/^>(.*)$/', '\1', $line);
$residues = '';
}
else {
$residues .= trim($line);
}
}
// add in the last sequence
$sql = "EXECUTE sel_gfftemp_un('%s')";
$result = tripal_core_chado_execute_prepared('sel_gfftemp_un', $sql, array($id));
if (!$result) {
watchdog('T_gff3_loader', 'Cannot find feature to assign FASTA sequence: %uname',
array('%uname' => $id), WATCHDOG_WARNING);
}
// if we have a feature then add the residues
else {
$feature = db_fetch_object($result);
$values = array('residues' => $residues);
$match = array('feature_id' => $feature->feature_id);
$options = array('statement_name' => 'upd_feature_re');
tripal_core_chado_update('feature', $match, $values, $options);
}
}
| tripal_feature_load_gff3_target | ( | $ | feature, |
| $ | tags, | ||
| $ | target_organism_id, | ||
| $ | target_type, | ||
| $ | create_target, | ||
| $ | attr_locgroup | ||
| ) |
Definition at line 1802 of file gff_loader.inc.
{
// format is: "target_id start end [strand]", where strand is optional and may be "+" or "-"
$matched = preg_match('/^(.*?)\s+(\d+)\s+(\d+)(\s+[\+|\-])*$/', trim($tags['Target'][0]), $matches);
// the organism and type of the target may also be specified as an attribute. If so, then get that
// information
$gff_target_organism = array_key_exists('target_organism', $tags) ? $tags['target_organism'][0] : '';
$gff_target_type = array_key_exists('target_type', $tags) ? $tags['target_type'][0] : '';
// if we have matches and the Target is in the correct format then load the alignment
if ($matched) {
$target_feature = $matches[1];
$start = $matches[2];
$end = $matches[3];
// if we have an optional strand, convert it to a numeric value.
if ($matches[4]) {
if (preg_match('/^\+$/', trim($matches[4]))) {
$target_strand = 1;
}
elseif (preg_match('/^\-$/', trim($matches[4]))) {
$target_strand = -1;
}
else {
$target_strand = 0;
}
}
else {
$target_strand = 0;
}
$target_fmin = $start - 1;
$target_fmax = $end;
if ($end < $start) {
$target_fmin = $end - 1;
$target_fmax = $start;
}
// default the target organism to be the value passed into the function, but if the GFF
// file species the target organism then use that instead.
$t_organism_id = $target_organism_id;
if ($gff_target_organism) {
// get the genus and species
$success = preg_match('/^(.*?):(.*?)$/', $gff_target_organism, $matches);
if ($success) {
$values = array(
'genus' => $matches[1],
'species' => $matches[2],
);
$options = array('statement_name' => 'sel_organism_gesp');
$torganism = tripal_core_chado_select('organism', array('organism_id'), $values, $options);
if (count($torganism) == 1) {
$t_organism_id = $torganism[0]->organism_id;
}
else {
watchdog('T_gff3_loader', "Cannot find organism for target %target.",
array('%target' => $gff_target_organism), WATCHDOG_WARNING);
$t_organism_id = '';
}
}
else {
watchdog('T_gff3_loader', "The target_organism attribute is improperly formatted: %target.
It should be target_organism=genus:species.",
array('%target' => $gff_target_organism), WATCHDOG_WARNING);
$t_organism_id = '';
}
}
// default the target type to be the value passed into the function, but if the GFF file
// species the target type then use that instead
$t_type_id = '';
if ($target_type) {
$values = array(
'name' => $target_type,
'cv_id' => array(
'name' => 'sequence',
)
);
$options = array('statement_name' => 'sel_cvterm_nacv');
$type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
if (count($type) == 1) {
$t_type_id = $type[0]->cvterm_id;
}
else {
watchdog('T_gff3_loader', "The target type does not exist in the sequence ontology: %type. ",
array('%type' => $target_type), WATCHDOG_ERROR);
exit;
}
}
if ($gff_target_type) {
$values = array(
'name' => $gff_target_type,
'cv_id' => array(
'name' => 'sequence',
)
);
$options = array('statement_name' => 'sel_cvterm_nacv');
$type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
if (count($type) == 1) {
$t_type_id = $type[0]->cvterm_id;
}
else {
watchdog('T_gff3_loader', "The target_type attribute does not exist in the sequence ontology: %type. ",
array('%type' => $gff_target_type), WATCHDOG_WARNING);
$t_type_id = '';
}
}
// we want to add a featureloc record that uses the target feature as the srcfeature (landmark)
// and the landmark as the feature.
tripal_feature_load_gff3_featureloc($feature, $organism, $target_feature, $target_fmin,
$target_fmax, $target_strand, $phase, $attr_fmin_partial, $attr_fmax_partial, $attr_residue_info,
$attr_locgroup, $t_type_id, $t_organism_id, $create_target, TRUE);
}
// the target attribute is not correctly formatted
else {
watchdog('T_gff3_loader', "Could not add 'Target' alignment as it is improperly formatted: '%target'",
array('%target' => $tags['Target'][0]), WATCHDOG_ERROR);
}
}
1.7.4