danmaclean

tracks:
    - id: 1
      name: My Gene Models Track
      type: ModelsTrack
      path: Gene Models
      data: /features/annoj/1
      showControls: true
      height: 80
    - id: 2
      name: Reads from an RDBMS provided experiment loaded via gff

danmaclean

Chr1  TAIR9	gene	3631	5899	.	+	.	ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
Chr1	TAIR9	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
Chr1	TAIR9	exon	3631	3913	.	+	.	Parent=AT1G01010.1

danmaclean

{ 
"recipient": "[email protected]", 
"evidence": "http://google.com", 
"issued_on": "2012-05-21", 
"badge": { "version": "1.0.0", "name": "command line user", 
  "image": "http://tsltraining.tsl.ac.uk/wp-content/uploads/2013/04/unix.png", 
	"description": "Has displayed expertise in command line use.", 
	"criteria": "http://tsltraining.tsl.ac.uk", 
	"issuer": { 
		"origin": "http://www.tsl.ac.uk", 

danmaclean

{ 
"recipient": "[email protected]", 
"evidence": "http://google.com", 
"issued_on": "2012-05-21", 
"badge": { "version": "1.0.0", "name": "command line user", 
  "image": "http://tsltraining.tsl.ac.uk/wp-content/uploads/2013/04/unix.png", 
	"description": "Has displayed expertise in command line use.", 
	"criteria": "http://tsltraining.tsl.ac.uk", 
	"issuer": { 
		"origin": "http://www.tsl.ac.uk", 

danmaclean

n95829:gee_fu-experimental-6 macleand$ rake db:migrate
DEPRECATION WARNING: You have Rails 2.3-style plugins in vendor/plugins! Support for these plugins will be removed in Rails 4.0. Move them out and bundle them in your Gemfile, or fold them in to your app as lib/myplugin/* and config/initializers/myplugin.rb. See the release notes for more on this: http://weblog.rubyonrails.org/2012/1/4/rails-3-2-0-rc2-has-been-released. (called from <top (required)> at /Users/macleand/Downloads/gee_fu-experimental-6/Rakefile:7)
==  AddOrganismToGenome: migrating ============================================
-- add_column(:genomes, :organism_id, :integer)
   -> 0.0061s
-- add_foreign_key(:genomes, :organisms)
   -> 0.0252s
-- change_column(:genomes, :organism_id, :integer, {:null=>false})
   -> 0.0073s
==  AddOrganismToGenome: migrated (0.1046s) ===================================

danmaclean

require 'bio'
some_text = "aatgacccgt" * 10
seq = Bio::Sequence::NA.new(some_text)
puts seq.to_fasta("seq_name", 60)

danmaclean

  def to_gff(extra = {})
    #arr should be hash of keys and values to add to the group attributes
    #can't use symbols as keys
    arr = extra.to_a
    
    gff = Bio::GFF::GFF3::Record.new(
    seqid = Reference.find(self.reference_id).name,
    source = self.source,
    feature = self.feature,
    start = self.start,

danmaclean

  def to_gff(extra = {})
    #arr should be hash of keys and values to add to the group attributes
    arr = extra.to_a
    
    gff = Bio::GFF::GFF3::Record.new(
    seqid = Reference.find(self.reference_id).name,
    source = self.source,
    feature = self.feature,
    start = self.start,
    stop = self.end,

danmaclean

        ref = Reference.find(:first, :conditions => ["name = ? AND genome_id = ?", "#{ record.seqname }", "#{@experiment.genome_id}"])

        feature = Feature.new(
          :group => "#{attribute}",
          :feature => "#{record.feature}",
          :source => "#{record.source}",
          :start => "#{record.start}",
          :end => "#{record.end}", 
          :strand => "#{record.strand}",
          :phase => "#{record.frame}",

danmaclean

      File.open( "#{@experiment.gff_file.path}" ).each do |line|
        next if line =~ /^#/
        break if line =~ /^##fasta/ or line =~ /^>/
        record = Bio::GFF::GFF3::Record.new(line)