function tripal_get_fasta_defline
| 2.x tripal_feature.api.inc | tripal_get_fasta_defline($feature, $notes = '', $featureloc = NULL, $type = '', $length = 0) |
| 3.x tripal_chado.module.DEPRECATED.api.inc | tripal_get_fasta_defline($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.
$length: Optional: the length of the sequence.
Return value
A string of the format: uniquename|name|type|feature_id or if an alignment: srcfeature_name:fmin..fmax[+-]; alignment of uniquename|name|type|feature_id.
- tripal_feature_load_featureloc_sequences in legacy/
tripal_feature/ theme/ tripal_feature.theme.inc - Get the sequence this feature is located on
- tripal_feature_sequence.tpl.php in legacy/
tripal_feature/ theme/ templates/ tripal_feature_sequence.tpl.php
File
- tripal_chado/
api/ modules/ tripal_chado.module.DEPRECATED.api.inc, line 829 - These api functions are deprecated, if your site is currently using them please update your code with the newer tripal_chado functions.
Code
function tripal_get_fasta_defline($feature, $notes = '', $featureloc = null, $type = '', $length = 0) {
chado_get_fasta_defline($feature, $notes, $featureloc, $type, $length);
}