Retrieves the bulk sequences for a given feature.

Parameters

$options: An associative array of options for selecting a feature. Valid keys include:

• org_commonname: The common name of the organism for which sequences should be retrieved
• genus: The genus of the organism for which sequences should be retrieved
• species: The species of the organism for which sequences should be retrieved
• analysis_name: The name of an analysis to which sequences belong. Only those that are associated with the analysis will be retrieved.
• type: The type of feature (a sequence ontology term).
• feature_name: the name of the feature. Can be an array of feature names.
• feature_uname: the uniquename of the feature. Can be an array of feature unique names.
• upstream: An integer specifing the number of upstream bases to include in the output
• downstream: An integer specifying the number of downstream bases to include in the output.
• derive_from_parent: Set to '1' if the sequence should be obtained from the parent to which this feature is aligned.
• aggregate: Set to '1' if the sequence should only contain sub features, excluding intro sub feature sequence. For example, set this option to obtain just the coding sequence of an mRNA.
• sub_feature_types: Only include sub features (or child features) of the types provided in the array
• relationship_type: If a relationship name is provided (e.g. sequence_of) then any sequences that are in relationships of this type with matched sequences are also included
• relationship_part: If a relationship is provided in the preceeding argument then the rel_part must be either 'object' or 'subject' to indicate which side of the relationship the matched features belong
• width: Indicate the number of bases to use per line. A new line will be added after the specified number of bases on each line.
• is_html: Set to '1' if the sequence is meant to be displayed on a web page. This will cause a <br> tag to separate lines of the FASTA sequence.

Return value

Returns an array of sequences. The sequences will be in an array with the following keys for each sequence: 'types' => an array of feature types that were used to derive the sequence (e.g. from an aggregated sequence) 'upstream' => the number of upstream bases in the sequence 'downstream' => the number of downstream bases in the sequence 'defline' => the definintion line used to create a FASTA sequence 'residues' => the residues 'featureloc_id' => the featureloc_id if from an alignment

File

tripal_chado/api/modules/tripal_chado.module.DEPRECATED.api.inc, line 799

These api functions are deprecated, if your site is currently using them please update your code with the newer tripal_chado functions.

Code

function tripal_get_bulk_feature_sequences($options) {
  chado_get_bulk_feature_sequences($options);
}