Class: BlastTableResult

Inherits:
BlastResult show all
Defined in:
lib/scbi_blast/blast_table_result.rb

Overview

Extracts results from blast table’s file and uses it to create instances of “BlastQuery” and “BlastHit”

Instance Attribute Summary

Attributes inherited from BlastResult

#querys

Instance Method Summary collapse

Methods inherited from BlastResult

#compare?, #empty?, #find_query, #inspect, #size

Constructor Details

#initialize(input) ⇒ BlastTableResult

Parser initialization



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# File 'lib/scbi_blast/blast_table_result.rb', line 31

def initialize(input)

  super(input)

  return if input.empty?
  
  if input.is_a?(Array)
    lines=input

  else

    fich = File.open(input,'r')
    lines = fich.readlines
    fich.close

  end
  parse(lines)
end

Instance Method Details

#parse(lines) ⇒ Object 



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# File 'lib/scbi_blast/blast_table_result.rb', line 50

def parse(lines)
  
  with_comments=false

  if lines.first.index('#')==0 
      with_comments=true
      if !(lines.last =~ /# BLAST processed (\d+) queries/)
          raise "Blast didn't processed your queries"
      end
  end
  
  query_name=''

  lines.each do |line|

    line.chomp! #delete end of line

    if line =~ /^\s*#/
      if line =~ /^#\sQuery:\s+(.+)$/
        query_name = $1
      elsif line =~ /^#\s0\shits\sfound$/
        @querys.push BlastQuery.new(query_name)
      end
      
      # 0 hits found

    else
      params = line.split(/\t+/)

      # puts "Extracted #{params[0]} #{params[1]} #{params[2]} #{params[3]} #{params[4]} #{params[5]} #{params[6]} #{params[7]} #{params[8]} #{params[9]} #{params[10]} #{params[11]}"
      #         Options 6, 7, and 10 can be additionally configured to produce
      #   a custom format specified by space delimited format specifiers.
      #   The supported format specifiers are:
      #            qseqid means Query Seq-id
      #               qgi means Query GI
      #              qacc means Query accesion
      #            sseqid means Subject Seq-id
      #         sallseqid means All subject Seq-id(s), separated by a ';'
      #               sgi means Subject GI
      #            sallgi means All subject GIs
      #              sacc means Subject accession
      #           sallacc means All subject accessions
      #            qstart means Start of alignment in query
      #              qend means End of alignment in query
      #            sstart means Start of alignment in subject
      #              send means End of alignment in subject
      #              qseq means Aligned part of query sequence
      #              sseq means Aligned part of subject sequence
      #            evalue means Expect value
      #          bitscore means Bit score
      #             score means Raw score
      #            length means Alignment length
      #                        pident means Percentage of identical matches
      #            nident means Number of identical matches
      #          mismatch means Number of mismatches
      #          positive means Number of positive-scoring matches
      #           gapopen means Number of gap openings
      #              gaps means Total number of gaps
      #              ppos means Percentage of positive-scoring matches
      #            frames means Query and subject frames separated by a '/'
      #            qframe means Query frame
      #            sframe means Subject frame
      #   When not provided, the default value is:
      #   'qseqid sseqid pident length mismatch gapopen qstart qend sstart send
      #   evalue bitscore', which is equivalent to the keyword 'std'

      # if  the query doesn't exist, then create a new one,
      # else the hit will be added to the last query

      qseqid,sacc,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,score,qframe,sframe,qseq,sseq,qlen,slen,stitle = params
      
      # if format6 
      #if !with_comments and query_name!=qseqid
      #    @querys.push BlastQuery.new(query_name)
      #    query_name=qseqid
      #end

      # creates the hit
      hit = BlastHit.new(qstart,qend,sstart,send)

      hit.align_len=length
      hit.ident=pident

      hit.gaps=gapopen
      hit.mismatches=mismatch
      hit.e_val=evalue
      hit.bit_score=bitscore

      hit.score = score
      hit.q_frame = qframe
      hit.s_frame = sframe

      hit.subject_id = sacc
      hit.full_subject_length=slen # era 0
      hit.definition=stitle # era sacc
      hit.acc=sacc
      hit.q_seq=qseq
      hit.s_seq=sseq
      hit.q_len=qlen
      hit.s_len=slen
      

      query=find_query(@querys,qseqid)

      if (query)   #if it is a new query, it is created and added
        query.add_hit(hit)

      else      # else the hit is added in last query added
        query = BlastQuery.new(qseqid)
        query.add_hit(hit)
        @querys.push query
      end

      query.full_query_length=qlen

      #Description

      # read_blast_tab read tabular BLAST format created with blast_seq and written to file with write_blast - or with blastall and the -m 8 or -m 9 switch.
      #           Each column in the table corresponds to the following keys:
      #
      #              1. Q_ID - Query ID.
      #              2. S_ID - Subject ID.
      #              3. IDENT - Identity (%).
      #              4. ALIGN_LEN - Alignment length.
      #              5. MISMATCHES - Number of mismatches.
      #              6. GAPS - Number of gaps.
      #              7. Q_BEG - Query begin.
      #              8. Q_END - Query end.
      #              9. S_BEG - Subject begin.
      #             10. S_END - Subject end.
      #             11. E_VAL - Expect value.
      #             12. BIT_SCORE - Bit score.
      #
      #           Furthermore, two extra keys are added to the record:
      #
      #               * STRAND - Strand.
      #               * REC_TYPE - Record type.
    end
  end

  #inspect

end