Dan MacLean danmaclean
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| 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 |
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| 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
/ badge.json
Last active
December 16, 2015 10:38
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| { | |
| "recipient": "earner.name@gmail.com", | |
| "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", |
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| { | |
| "recipient": "maclean.daniel@gmail.com", | |
| "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", |
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| 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) =================================== |
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| require 'bio' | |
| some_text = "aatgacccgt" * 10 | |
| seq = Bio::Sequence::NA.new(some_text) | |
| puts seq.to_fasta("seq_name", 60) |
danmaclean
/ gist:5426143
Created
April 20, 2013 14:23
Feature#to_gff method improved for adding any other stuff from the database
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| 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, |
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| 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
/ gist:5437571
Created
April 22, 2013 19:00
finding a reference and creating the feature in experiments_controller.rb (lines 76 - 93)
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| 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
/ gist:5437636
Created
April 22, 2013 19:08
Poor handling of empty lines (non chomping of line!) in experiments_controller.rb lines 51 - 54
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| 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) |
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