Class: PubliSci::Parsers::MAF

Inherits:
Object
  • Object
show all
Extended by:
Base
Defined in:
lib/publisci/parsers/maf.rb

Constant Summary collapse

COLUMN_NAMES = 
%w{ Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS  dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1  Match_Norm_Seq_Allele2  Tumor_Validation_Allele1  Tumor_Validation_Allele2  Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase  Sequence_Source Validation_Method Score BAM_File  Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID patient_id sample_id}

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Base

each, process_record, valid?

Class Method Details

.process_record(rec) ⇒ Object 



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# File 'lib/publisci/parsers/maf.rb', line 15

def self.process_record(rec)
  ::CSV.parse(rec, {col_sep: "\t"}).flatten[0..(COLUMN_NAMES.length-3)]
end

.valid?(line) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/publisci/parsers/maf.rb', line 7

def self.valid?(line)
  not (line[0] == "#" || line[0..3] == "Hugo")
end

Instance Method Details

#enum_method ⇒ Object 



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# File 'lib/publisci/parsers/maf.rb', line 11

def enum_method
  :each_line
end