Class: Bio::PSORT::WoLF_PSORT::Wrapper

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/psort/wolf_psort_wrapper.rb

Constant Summary collapse

ORGANISM_TYPES = 
%w(plant animal fungi)
SUMMARY_EXECUTABLE_NAME = 
'runWolfPsortSummary'

Instance Method Summary collapse

Instance Method Details

#run(amino_acid_sequence_string, organism_type) ⇒ Object

Given an amino acid sequence as a String and an organism type (plasnt/animal/fungi) as a String, run a local version of WoLF_PSORT (which is assumed to be in the executable path) and return a parsed report. Return nil if something untoward happens.

A known problem is that it doesn’t work on sequences that are too short. For instance the sequence MRTLKTEVEKGFLSTMFVQELATPKG prints out an error on the command line: Modification of non-creatable array value attempted, subscript -1 at /home/ben/bioinfo/WoLFPSORT_package_v0.2/bin/psortModifiedForWolfFiles/psortModules/PsortFastaReader.pm line 440, <STDIN> line 1.



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# File 'lib/bio/appl/psort/wolf_psort_wrapper.rb', line 19

def run(amino_acid_sequence_string, organism_type)
  fasta = ">wolf\n#{amino_acid_sequence_string}"
  
  output = Bio::Command.query_command([SUMMARY_EXECUTABLE_NAME, organism_type], fasta)
  return nil if output == '' or output.nil? # happens when the sequence is too short
  return Bio::PSORT::WoLF_PSORT::Report.parse_from_summary(organism_type, output.split("\n")[1])
end