Class: Bio::Ngs::Cufflinks::Compare

Inherits:
Object
  • Object
show all
Includes:
Command::Wrapper
Defined in:
lib/bio/appl/ngs/cufflinks.rb

Overview

cuffcompare v1.0.2 (2335)

Usage: cuffcompare [-r <reference_mrna.gtf>] [-R] [-T] [-V] [-s <seq_path>]

   [-o <outprefix>] [-p <cprefix>]
   {-i <input_gtf_list> | <input1.gtf> [<input2.gtf> .. <inputN.gtf>]}

Cuffcompare provides classification, reference annotation mapping and various
statistics for Cufflinks transfrags.
Cuffcompare clusters and tracks transfrags across multiple samples, writing
matching transcripts (intron chains) into <outprefix>.tracking, and a GTF
file <outprefix>.combined.gtf containing a nonredundant set of transcripts
across all input files (with a single representative transfrag chosen
for each clique of matching transfrags across samples).

Options: -i provide a text file with a list of Cufflinks GTF files to process instead

of expecting them as command line arguments (useful when a large number
of GTF files should be processed)

-r a set of known mRNAs to use as a reference for assessing

the accuracy of mRNAs or gene models given in <input.gtf>

-R for -r option, reduce the set of reference transcripts to

only those found to overlap any of the input loci

-M discard (ignore) single-exon transfrags and reference transcripts -N discard (ignore) single-exon reference transcripts

-s <seq_path> can be a multi-fasta file with all the genomic sequences or

a directory containing multiple single-fasta files (one file per contig);
lower case bases will be used to classify input transcripts as repeats

-d max distance (range) for grouping transcript start sites (100) -p the name prefix to use for consensus transcripts in the

<outprefix>.combined.gtf file (default: 'TCONS')

-C include the “contained” transcripts in the .combined.gtf file -G generic GFF input file(s) (do not assume Cufflinks GTF) -T do not generate .tmap and .refmap files for each input file -V verbose processing mode (showing all GFF parsing warnings)

Class Method Summary collapse

Methods included from Command::Wrapper

#class_name, #default_options, included, #initialize, #normalize_params, #options, #options=, #output, #params, #params=, #path, #path=, #pipe_ahead, #pipe_ahead=, #pipe_ahead?, #program, #reset_params, #run, #sub_program, #thor_task, #to_cmd_ary, #use_aliases?

Class Method Details

.build_compare_kb(gtf) ⇒ Object

Dump an hash of associations from a GTF file generated from CuffCompare gene_id: transcript_id, gene_name, oid, nearest_ref

gene_id example: :XLOC_000001=>{:gene_name=>:RP11-304M2.1, :transcripts=>{:TCONS_00000001=>{:oid=>:ENST00000519787, :nearest_ref=>:ENST00000519787}}}

the others are just plain hash transcript_id: gene_id, gene_name, oid, nearest_ref gene_name: gene_id, transcript_id, oid, nearest_ref oid: gene_id, transcript_id, gene_name, nearest_ref nearest_ref: gene_id, transcript_id, gene_name, oid Note:exons and coordinates are not saved.



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# File 'lib/bio/appl/ngs/cufflinks.rb', line 555

def build_compare_kb(gtf)
  unless File.exists?(gtf)
    STDERR.puts "File #{gtf} doesn't exist."
    return nil
  end

  dict = {} #build an hash with the combinations of data extracted from GTF file, XLOC, TCONS, ENST, SYMBOL
  File.open(gtf,'r') do |f|
    f.lines do |line|
      line=~/gene_id (.*?);/
      gene_id = $1.gsub(/"/,'').to_sym
      line=~/transcript_id (.*?);/
      transcript_id = $1.gsub(/"/,'').to_sym
      line=~/gene_name (.*?);/
      gene_name = $1.gsub(/"/,'').to_sym
      line=~/oId (.*?);/
      oid=$1.gsub(/"/,'').to_sym
      line=~/nearest_ref (.*?);/
      nearest_ref = $1.gsub(/"/,'').to_sym
      unless dict.key?(gene_id)
        dict[gene_id]={:gene_name=>gene_name,:transcripts=>{}}
      end
      unless dict[gene_id][:transcripts].key?(transcript_id)
        dict[gene_id][:transcripts][transcript_id]={:odi=>oid, :nearest_ref=>nearest_ref}
      end
      dict[transcript_id]={:gene_id=>gene_id, :gene_name=>gene_name, :odi=>oid, :nearest_ref=>nearest_ref}
      dict[gene_name]={:gene_id=>gene_id, :transcript_id=>transcript_id, :odi=>oid, :nearest_ref=>nearest_ref}
      dict[oid]={:gene_id=>gene_id, :transcript_id=>transcript_id, :gene_name=>gene_name, :nearest_ref=>nearest_ref}
      dict[nearest_ref]={:gene_id=>gene_id, :transcript_id=>transcript_id, :odi=>oid, :gene_name=>gene_name}
    end#lines
  end#file
  kb_filename = kb_name(gtf)
  File.open(kb_filename,'w') do |fkb|
    #fkb.write(dict.to_json)
    Marshal.dump(dict,fkb)
  end #fkb
  dict
end

.exists_kb?(gtf) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/appl/ngs/cufflinks.rb', line 542

def exists_kb?(gtf)
  File.exists?(kb_name(gtf))
end

.kb_name(gtf) ⇒ Object 



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# File 'lib/bio/appl/ngs/cufflinks.rb', line 538

def kb_name(gtf)
  gtf.sub(/\.[a-zA-Z0-9]*$/,".kb")
end

.load_compare_kb(gtf) ⇒ Object

Return the hash of associations gene_id: transcript_id, gene_name, oid, nearest_ref transcript_id: gene_id, gene_name, oid, nearest_ref gene_name: gene_id, transcript_id, oid, nearest_ref oid: gene_id, transcript_id, gene_name, nearest_ref nearest_ref: gene_id, transcript_id, gene_name, oid



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# File 'lib/bio/appl/ngs/cufflinks.rb', line 600

def load_compare_kb(gtf)
  #TODO rescue Exceptions
  kb_filename = kb_name(gtf)
  gtf_kb = File.open(kb_filename,'r') do |kb_dump|
    Marshal.load(kb_dump)
  end
end