tripal/tripal_feature/tripal_feature.drush.inc

<?php

/**
 * @file
 * Contains function relating to drush-integration of this module.
 */

/**
 * Describes each drush command implemented by the module
 *
 * @return
 *   The first line of description when executing the help for a given command
 */
function tripal_feature_drush_help($command) {
  switch ($command) {
    case 'drush:tripal-get_sequence':
      return dt('Prints sequences that match specified categories.');
  }
}

/**
 * Registers a drush command and constructs the full help for that command
 *
 * @return
 *   And array of command descriptions
 */
function tripal_feature_drush_command() {
  $items = array();
  $items['tripal-get-sequence'] = array(
    'description' => dt('Prints sequences that match specified categories.'),
    'options'    => array(
      'org'      => dt('The organism\'s common name. If specified, features for this organism will be retrieved.'),
      'genus'    => dt('The organism\'s genus. If specified, features for all organism with this genus will be retrieved.'),
      'species'  => dt('The organism\'s species name. If specified, features for this all organism with this species will be retrieved.'),
      'analysis' => dt('The analysis name. If specified, features for this analysis will be retrieved.'),
      'type'     => dt('The type of feature to retrieve (e.g. mRNA). All features that match this type will be retrieved.'),
      'name'     => dt('The name of the feature to retrieve.'),
      'up'       => dt('An integer value specifying the number of upstream bases to include.'),
      'down'     => dt('An integer value specifying the number of downstream bases to incldue.'),
      'out'      => dt('The output format. Valid options are "fasta_html", "fasta_txt" and raw.'),
      'parent'   => dt('Set this argument to 1 to retrieve the sequence from the parent in an alignment rather than the residues column of the feature itself.'),
      'agg'      => dt('Set this argument to 1 to aggregate sub features into a single sequence.  This is useful, for example, for obtaining CDS sequence from an mRNA'),
      'child'    => dt('Set this argument to the sequence ontology term for the children to aggregate.  This is useful in the case where a gene has exons as well as CDSs and UTRs.  You may sepcify as many feature types as desired by separating each with a single comma (no spaces).'),
      'object_rel'  => dt('Retreives the sequence of any features in relationship with the matched features from other criteria where the feature is the subject of the relationship'),
      'subject_rel' => dt('Retreives the sequence of any features in relationship with the matched features from other criteria where the feature is the object of the relationship. '),
    ),
    'examples' => array(
      'Standard example' => 'drush tripal-current-job',
    ),
    'aliases' => array('trp-get-seq'),
  );
  $items['tripal-feature-sync'] = array(
    'description' => dt('Syncs an individual feature.'),
    'options'   => array(
      'id'    => dt('The feature ID of the feature to sync'),
    ),
    'examples' => array(
      'Standard example' => 'drush tripal-feature-sync --id=48273',
    ),
    'aliases' => array('trp-fsync'),
  );
  return $items;
}

/**
 * Executes jobs in the Tripal Jobs Queue
 *
 * NOTE: The following code is executed when drush 'trpjob-run' or 'drush tripal-launch-jobs' is called
 */
function drush_tripal_feature_tripal_get_sequence() {

  $org_commonname = drush_get_option('org');  
  $genus = drush_get_option('genus');
  $species = drush_get_option('species');
  $analysis_name = drush_get_option('analysis');  
  $type = drush_get_option('type');
  $feature_name = drush_get_option('name');
  $upstream = drush_get_option('up');
  $downstream = drush_get_option('down');
  $output_format = drush_get_option('out');
  $derive_from_parent = drush_get_option('parent');
  $aggregate = drush_get_option('agg');
  $child = drush_get_option('child');
  $object_rel = drush_get_option('object_rel');
  $subject_rel = drush_get_option('subject_rel');
    
  tripal_feature_seq_extract_get_features($org_commonname, $genus, $species, $analysis_name, 
    $type, $feature_name, $upstream, $downstream, $output_format, $derive_from_parent, 
    $aggregate, $child, $subject_rel, $object_rel);   
}
/*
 * 
 */
function drush_tripal_feature_sync() {
  $feature_id = drush_get_option('id');  
  tripal_feature_sync_feature($feature_id);
}