Chado Feature

Collaboration diagram for Chado Feature:

Functions
	chado_autocomplete_feature ($string='')
	chado_reverse_compliment_sequence ($sequence)
	chado_get_feature_sequences ($feature, $options)
	chado_get_bulk_feature_sequences ($options)
	chado_get_fasta_defline ($feature, $notes='', $featureloc=NULL, $type='', $length=0)
	chado_get_location_string ($featureloc)

Detailed Description

Provides API functions specifically for managing feature records in Chado especially retrieving relationships and sequences derived from relationships and feature alignments.

Function Documentation

chado_autocomplete_feature()

chado_autocomplete_feature

(

$string = ''

)

Used for autocomplete in forms for identifying for publications.

Parameters

$field	The field in the publication to search on.
$string	The string to search for.

Returns

A json array of terms that begin with the provided string.

chado_get_bulk_feature_sequences()

chado_get_bulk_feature_sequences

(

$options

)

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 preceding 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 tag to separate lines of the FASTA sequence.

Returns

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 definition line used to create a FASTA sequence 'residues' => the residues 'featureloc_id' => the featureloc_id if from an alignment

chado_get_fasta_defline()

chado_get_fasta_defline	(		$feature,
			$notes = '',
			$featureloc = NULL,
			$type = '',
			$length = 0
	)

Returns a definition line that can be used in a FASTA file.

Parameters

$feature	A single feature object containing all the fields from the chado.feature table. Best case is to provide an object generated by the chado_generate_var() function.
$notes	Optional: additional notes to be added to the definition line.
$featureloc	Optional: a single featureloc object generated using chado_generate_var that contains a record from the chado.featureloc table. Provide this if the sequence was obtained by using the alignment rather than from the feature.residues column.
$type	Optional: the type of sequence. By default the feature type is used.
$length	Optional: the length of the sequence.

Returns

A string of the format: uniquename|name|type|feature_id or if an alignment: srcfeature_name:fmin..fmax[+-]; alignment of uniquename|name|type|feature_id.

chado_get_feature_sequences()

chado_get_feature_sequences	(		$feature,
			$options
	)

Retrieves the sequences for a given feature.

If a feature has multiple alignments or multiple relationships then multiple sequences will be returned.

Parameters

$feature

An associative array describing the feature. Valid keys include: feature_id: The feature_id of the feature for which the sequence will be retrieved. name: The feature name. This will appear on the FASTA definition line. parent_id: (optional) only retrieve a sequence if 'derive_from_parent' is true and the parent matches this ID. featureloc_id: (optional) only retrieve a sequence if 'derive_from_parent' is true and the alignment is defined with this featureloc_id.

$options

An associative array of options. Valid keys include: 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 tag to separate lines of the FASTA sequence. 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. 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. 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 preceding argument then the rel_part must be either 'object' or 'subject' to indicate which side of the relationship the matched features belong.

Returns

an array of matching sequence in 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 included in the sequence
• downstream: the number of downstream bases included in the sequence
• defline: the definition line used to create a FASTA sequence
• residues: the residues
• featureloc_id: the featureloc_id if the sequences is from an alignment

chado_get_location_string()

chado_get_location_string

(

$featureloc

)

Returns a string representing a feature location in an alignment.

Parameters

$featureloc

A single featureloc object generated using chado_generate_var that contains a record from the chado.featureloc table.

Returns

A string of the format: uniquename:featurelocmin..featurelocmax.strand

chado_reverse_compliment_sequence()

chado_reverse_compliment_sequence

(

$sequence

)

Performs a reverse compliment of a nucleotide sequence.

Parameters

$sequence

The nucelotide sequence.

Returns

an upper-case reverse complemented sequence.