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