Class: Bio::PolyploidTools::SNPMutant

Inherits:
SNPSequence show all
Defined in:
lib/bio/PolyploidTools/SNPMutant.rb

Instance Attribute Summary collapse

Attributes inherited from SNPSequence

#sequence_original

Attributes inherited from SNP

#chromosome, #container, #errors, #exon_list, #flanking_size, #gene, #genomes_count, #hit_count, #ideal_max, #ideal_min, #max_hits, #orientation, #original, #original_name, #position, #primer_3_min_seq_length, #repetitive, #snp, #snp_in, #snp_type, #template_sequence, #use_reference, #variation_free_region

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from SNP

#add_exon, #aligned_sequences, #aligned_sequences_fasta, #aligned_snp_position, #covered_region, #cut_and_pad_sequence_to_primer_region, #cut_sequence_to_primer_region, #exon_for_chromosome, #exon_sequences, #get_snp_position_after_trim, #get_target_sequence, #initialize, #left_padding, #local_position, #mask_aligned_chromosomal_snp, #padded_position, #parental_sequences, parseVCF, #primer_3_all_strings, #primer_3_string, #primer_fasta_string, #primer_region, #return_primer_3_string, #reverse_complement_string, #right_padding, #sequences_to_align, #setTemplateFromFastaFile, #short_s, #snp_id_in_seq, #surrounding_exon_sequences, #surrounding_masked_chromosomal_snps, #surrounding_parental_sequences, #to_fasta, #to_polymarker_coordinates, #to_polymarker_sequence, #to_s

Constructor Details

This class inherits a constructor from Bio::PolyploidTools::SNP

Instance Attribute Details

#chr ⇒ Object

Returns the value of attribute chr.



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 10

def chr
  @chr
end

#contig ⇒ Object

Returns the value of attribute contig.



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 10

def contig
  @contig
end

#library ⇒ Object

Returns the value of attribute library.



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 10

def library
  @library
end

#parsed_flanking ⇒ Object

Returns the value of attribute parsed_flanking.



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 10

def parsed_flanking
  @parsed_flanking
end

#parsed_start ⇒ Object

Returns the value of attribute parsed_start.



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 10

def parsed_start
  @parsed_start
end

#region_size ⇒ Object

Returns the value of attribute region_size.



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 10

def region_size
  @region_size
end

Class Method Details

.parse(reg_str) ⇒ Object

Format: seqid,library,position,wt_base,mut_base IWGSC_CSS_1AL_scaff_1455974,Kronos2281,127,C,T



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 14

def self.parse(reg_str)
  reg_str.chomp!
  snp = SNPMutant.new

  arr = reg_str.split(",")
  
  throw SNPSequenceException.new "Need five fields to parse, and got #{arr.size} in #{reg_str}" if arr.size < 5
  
  snp.contig, snp.library, snp.position, snp.original, snp.snp, parsed_flanking, region_size = reg_str.split(",")
  snp.position = snp.position.to_i
  snp.gene = "EMPTY"
  begin
    toks = snp.contig.split('_')
    #1AL_1455974_Kronos2281_127C
    #snp.chr = contig.split('_')[2][0,2] #This parses the default from the IWGSC. We may want to make this a lambda  
    #snp.chr = toks[2][0,2]
    name = toks[2] + "_" + toks[4] + "_" + snp.library + "_" + snp.position.to_s 
    snp.gene = name
    snp.chromosome = toks[2][0,2]
    snp.chr = snp.chromosome
    
  rescue Exception => e
    $stderr.puts "WARN: snp.chr couldnt be set, the sequence id to parse was #{snp.contig}. We expect something like: IWGSC_CSS_1AL_scaff_1455974"
    snp.gene = "Error"
    $stderr.puts e
  end
  
  snp.flanking_size=100
  snp.region_size = region_size.to_i if region_size
  snp.flanking_size = parsed_flanking.to_i if parsed_flanking
  snp
end

Instance Method Details

#chromosome_genome ⇒ Object 



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 61

def chromosome_genome
  chr[1]
end

#chromosome_group ⇒ Object 



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 57

def chromosome_group
  chr[0]
end

#full_sequence ⇒ Object 



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 53

def full_sequence()
  self.template_sequence
end

#full_sequence=(seq) ⇒ Object 



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 47

def full_sequence=(seq)
  self.template_sequence = seq
  self.sequence_original = self.to_polymarker_sequence(self.flanking_size)
  self.parse_sequence_snp
end

#parse_sequence_snp ⇒ Object 



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# File 'lib/bio/PolyploidTools/SNPMutant.rb', line 70

def parse_sequence_snp
  pos = 0
  match_data = /(?<pre>\w*)\[(?<org>[ACGT])\/(?<snp>[ACGT])\](?<pos>\w*)/.match(sequence_original.strip)
  if match_data
    @position = Regexp.last_match(:pre).size + 1
    @original = Regexp.last_match(:org)
    @snp = Regexp.last_match(:snp)
    amb_base = Bio::NucleicAcid.to_IUAPC("#{@original}#{@snp}")
    @template_sequence = "#{Regexp.last_match(:pre)}#{amb_base}#{Regexp.last_match(:pos)}"
    
 end 
end