Class: Bio::Ngs::Cufflinks::Diff

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

Overview

cuffdiff v1.3.0 (3022)

Usage: cuffdiff [options] <transcripts.gtf> <sample1_hits.sam> <sample2_hits.sam> [… sampleN_hits.sam]

Supply replicate SAMs as comma separated lists for each condition: sample1_rep1.sam,sample1_rep2.sam,...sample1_repM.sam

General Options:

-o/--output-dir              write all output files to this directory              [ default:     ./ ]
--seed                       value of random number generator seed                 [ default:      0 ]
-T/--time-series             treat samples as a time-series                        [ default:  FALSE ]
-c/--min-alignment-count     minimum number of alignments in a locus for testing   [ default:   10 ]
--FDR                        False discovery rate used in testing                  [ default:   0.05 ]
-M/--mask-file               ignore all alignment within transcripts in this file  [ default:   NULL ]
-b/--frag-bias-correct       use bias correction - reference fasta required        [ default:   NULL ]
-u/--multi-read-correct      use 'rescue method' for multi-reads (more accurate)   [ default:  FALSE ]
-N/--upper-quartile-norm     use upper-quartile normalization                      [ default:  FALSE ]
-L/--labels                  comma-separated list of condition labels
-p/--num-threads             number of threads used during quantification          [ default:      1 ]

Advanced Options:

--library-type               Library prep used for input reads                     [ default:  below ]
-m/--frag-len-mean           average fragment length (unpaired reads only)         [ default:    200 ]
-s/--frag-len-std-dev        fragment length std deviation (unpaired reads only)   [ default:     80 ]
--num-importance-samples     number of importance samples for MAP restimation      [ default:   1000 ]
--num-bootstrap-samples      Number of bootstrap replications                      [ default:     20 ]
--bootstrap-fraction         Fraction of fragments in each bootstrap sample        [ default:    1.0 ]
--max-mle-iterations         maximum iterations allowed for MLE calculation        [ default:   5000 ]
--compatible-hits-norm       count hits compatible with reference RNAs only        [ default:   TRUE ]
--total-hits-norm            count all hits for normalization                      [ default:  FALSE ]
--poisson-dispersion         Don't fit fragment counts for overdispersion          [ default:  FALSE ]
-v/--verbose                 log-friendly verbose processing (no progress bar)     [ default:  FALSE ]
-q/--quiet                   log-friendly quiet processing (no progress bar)       [ default:  FALSE ]
--no-update-check            do not contact server to check for update availability[ default:  FALSE ]
--emit-count-tables          print count tables used to fit overdispersion         [ default:  FALSE ]
--max-bundle-frags           maximum fragments allowed in a bundle before skipping [ default: 500000 ]

Debugging use only:

--read-skip-fraction         Skip a random subset of reads this size               [ default:    0.0 ]
--no-read-pairs              Break all read pairs                                  [ default:  FALSE ]
--trim-read-length           Trim reads to be this long (keep 5' end)              [ default:   none ]
--cov-delta                  Maximum gap between bootstrap and IS                  [ default:   2.0  ]

Supported library types:

ff-firststrand
ff-secondstrand
ff-unstranded
fr-firststrand
fr-secondstrand
fr-unstranded (default)
transfrags

Class Method Summary collapse

Methods included from Utils

included

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

.genes(diff, gtf, options = {}) ⇒ Object

write a file with the information See process_de for options available Example: Bio::Ngs::Cufflinks::Diff.genes(“/Users/bonnalraoul/Desktop/RRep16giugno/DEPopNormNOTh2s1NOTh17s1_lane1-2-3-4-6-8/gene_exp.diff”, “/Users/bonnalraoul/Desktop/RRep16giugno/COMPARE_PopNormNOTh2s1NOTh17s1_lane1-2-3-4-6-8/ComparepPopNormNOTh2s1NOTh17s1_lane1-2-3-4-6-8.combined.gtf”, fold:0.5,min_samples:5,min_fpkm:0.5,z_scores:true, :regulated=>:up)



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# File 'lib/bio/appl/ngs/cufflinks.rb', line 299

def genes(diff, gtf, options={})
  process_de(diff, gtf, options) do |dict_info, diff_reference, gtf_kb, fpkm_values|
    #            puts diff_reference
    #            puts fpkm_values
    # "#{dict_info[:winner].first}\t#{gtf_kb[diff_reference][:gene_name]}\t#{fpkm_values.join("\t")}"
    #do not use th gtf kb
    "#{dict_info[:winner].first}\t#{dict_info[:gene_name]}\t#{fpkm_values.join("\t")}"
  end
end

.isoforms(diff, gtf, options = {}) ⇒ Object

write a file with the information See process_de for options available Example: Bio::Ngs::Cufflinks::Diff.isoforms(“/Users/bonnalraoul/Desktop/RRep16giugno/DEPopNormNOTh2s1NOTh17s1_lane1-2-3-4-6-8/isoform_exp.diff”, “/Users/bonnalraoul/Desktop/RRep16giugno/COMPARE_PopNormNOTh2s1NOTh17s1_lane1-2-3-4-6-8/ComparepPopNormNOTh2s1NOTh17s1_lane1-2-3-4-6-8.combined.gtf”, fold:0.5,min_samples:5,min_fpkm:0.5,z_scores:true, :regulated=>:up)



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# File 'lib/bio/appl/ngs/cufflinks.rb', line 288

def isoforms(diff, gtf, options={})
  process_de(diff, gtf, options) do |dict_info, diff_reference, gtf_kb, fpkm_values|
    "#{dict_info[:winner].first}\t#{gtf_kb[diff_reference][:nearest_ref]}_#{gtf_kb[diff_reference][:gene_name]}\t#{fpkm_values.join("\t")}"
  end
end

.offset_by_version(cufflinks_version) ⇒ Object 



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# File 'lib/bio/appl/ngs/cufflinks.rb', line 274

def offset_by_version(cufflinks_version)
  case cufflinks_version
  when "0.9.X"
    0
  when "1.0.X"
    1
  end
end

.version(diff) ⇒ Object

Return the version of CuffDiff used to produce the output



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# File 'lib/bio/appl/ngs/cufflinks.rb', line 260

def version(diff)
  #cufflink_version_offset = Bio::Ngs::Cufflinks.version
  f=File.open(diff,'r')
  header=f.readline #skip header
  f.close
  cufflink_version_offset = case header.split.size
  when 12
    "0.9.X"
  when 14
    Bio::Ngs::Cufflinks.version #latest
  end
end