Class: Bio::FastaFormat

Inherits:
DB show all
Defined in:
lib/bio/db/fasta.rb

Overview

Treats a FASTA formatted entry, such as:

>id and/or some comments                    <== comment line
ATGCATGCATGCATGCATGCATGCATGCATGCATGC        <== sequence lines
ATGCATGCATGCATGCATGCATGCATGCATGCATGC
ATGCATGCATGC

The precedent ‘>’ can be omitted and the trailing ‘>’ will be removed automatically.

Examples

f_str = <<END
>sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG
VPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME
GIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL
KLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC
IFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP
QWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES
>sce:YBR274W  CHK1; probable serine/threonine-protein kinase [EC:2.7.1.-] [SP:KB9S_YEAST]
MSLSQVSPLPHIKDVVLGDTVGQGAFACVKNAHLQMDPSIILAVKFIHVP
TCKKMGLSDKDITKEVVLQSKCSKHPNVLRLIDCNVSKEYMWIILEMADG
GDLFDKIEPDVGVDSDVAQFYFQQLVSAINYLHVECGVAHRDIKPENILL
DKNGNLKLADFGLASQFRRKDGTLRVSMDQRGSPPYMAPEVLYSEEGYYA
DRTDIWSIGILLFVLLTGQTPWELPSLENEDFVFFIENDGNLNWGPWSKI
EFTHLNLLRKILQPDPNKRVTLKALKLHPWVLRRASFSGDDGLCNDPELL
AKKLFSHLKVSLSNENYLKFTQDTNSNNRYISTQPIGNELAELEHDSMHF
QTVSNTQRAFTSYDSNTNYNSGTGMTQEAKWTQFISYDIAALQFHSDEND
CNELVKRHLQFNPNKLTKFYTLQPMDVLLPILEKALNLSQIRVKPDLFAN
FERLCELLGYDNVFPLIINIKTKSNGGYQLCGSISIIKIEEELKSVGFER
KTGDPLEWRRLFKKISTICRDIILIPN
END

f = Bio::FastaFormat.new(f_str)
puts "### FastaFormat"
puts "# entry"
puts f.entry
puts "# entry_id"
p f.entry_id
puts "# definition"
p f.definition
puts "# data"
p f.data
puts "# seq"
p f.seq
puts "# seq.type"
p f.seq.type
puts "# length"
p f.length
puts "# aaseq"
p f.aaseq
puts "# aaseq.type"
p f.aaseq.type
puts "# aaseq.composition"
p f.aaseq.composition
puts "# aalen"
p f.aalen

References

Direct Known Subclasses

FastaNumericFormat

Constant Summary collapse

DELIMITER =

Entry delimiter in flatfile text.

RS = "\n>"
DELIMITER_OVERRUN =

(Integer) excess read size included in DELIMITER.

1

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from DB

#exists?, #fetch, #get, open, #tags

Constructor Details

#initialize(str) ⇒ FastaFormat

Stores the comment and sequence information from one entry of the FASTA format string. If the argument contains more than one entry, only the first entry is used.



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# File 'lib/bio/db/fasta.rb', line 155

def initialize(str)
  @definition = str[/.*/].sub(/^>/, '').strip	# 1st line
  @data = str.sub(/.*/, '')				# rests
  @data.sub!(/^>.*/m, '')	# remove trailing entries for sure
  @entry_overrun = $&
end

Instance Attribute Details

#data ⇒ Object

The seuqnce lines in text.



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# File 'lib/bio/db/fasta.rb', line 148

def data
  @data
end

#definition ⇒ Object

The comment line of the FASTA formatted data.



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# File 'lib/bio/db/fasta.rb', line 145

def definition
  @definition
end

#entry_overrun ⇒ Object (readonly)

Returns the value of attribute entry_overrun.



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# File 'lib/bio/db/fasta.rb', line 150

def entry_overrun
  @entry_overrun
end

Instance Method Details

#aalen ⇒ Object

Returens the length of Bio::Sequence::AA.



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# File 'lib/bio/db/fasta.rb', line 245

def aalen
  self.aaseq.length
end

#aaseq ⇒ Object

Returens the Bio::Sequence::AA.



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# File 'lib/bio/db/fasta.rb', line 240

def aaseq
  Sequence::AA.new(seq)
end

#acc_version ⇒ Object

Returns accession number with version.



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# File 'lib/bio/db/fasta.rb', line 303

def acc_version
  identifiers.acc_version
end

#accession ⇒ Object

Returns an accession number.



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# File 'lib/bio/db/fasta.rb', line 291

def accession
  identifiers.accession
end

#accessions ⇒ Object

Parsing FASTA Defline (using #identifiers method), and shows accession numbers. It returns an array of strings.



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# File 'lib/bio/db/fasta.rb', line 298

def accessions
  identifiers.accessions
end

#comment ⇒ Object

Returns comments.



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# File 'lib/bio/db/fasta.rb', line 219

def comment
  seq
  @comment
end

#entry ⇒ Object Also known as: to_s

Returns the stored one entry as a FASTA format. (same as to_s)



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# File 'lib/bio/db/fasta.rb', line 163

def entry
  @entry = ">#{@definition}\n#{@data.strip}\n"
end

#entry_id ⇒ Object

Parsing FASTA Defline (using #identifiers method), and shows a possibly unique identifier. It returns a string.



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# File 'lib/bio/db/fasta.rb', line 277

def entry_id
  identifiers.entry_id
end

#gi ⇒ Object

Parsing FASTA Defline (using #identifiers method), and shows GI/locus/accession/accession with version number. If a entry has more than two of such IDs, only the first ID are shown. It returns a string or nil.



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# File 'lib/bio/db/fasta.rb', line 286

def gi
  identifiers.gi
end

#identifiers ⇒ Object

Parsing FASTA Defline, and extract IDs. IDs are NSIDs (NCBI standard FASTA sequence identifiers) or “:”-separated IDs. It returns a Bio::FastaDefline instance.



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# File 'lib/bio/db/fasta.rb', line 267

def identifiers
  unless defined?(@ids) then
    @ids = FastaDefline.new(@definition)
  end
  @ids
end

#length ⇒ Object

Returns sequence length.



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# File 'lib/bio/db/fasta.rb', line 225

def length
  seq.length
end

#locus ⇒ Object

Returns locus.



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# File 'lib/bio/db/fasta.rb', line 308

def locus
  identifiers.locus
end

#nalen ⇒ Object

Returens the length of Bio::Sequence::NA.



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# File 'lib/bio/db/fasta.rb', line 235

def nalen
  self.naseq.length
end

#naseq ⇒ Object

Returens the Bio::Sequence::NA.



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# File 'lib/bio/db/fasta.rb', line 230

def naseq
  Sequence::NA.new(seq)
end

#query(factory) ⇒ Object Also known as: fasta, blast

Executes FASTA/BLAST search by using a Bio::Fasta or a Bio::Blast factory object.

#!/usr/bin/env ruby
require 'bio'

factory = Bio::Fasta.local('fasta34', 'db/swissprot.f')
flatfile = Bio::FlatFile.open(Bio::FastaFormat, 'queries.f')
flatfile.each do |entry|
  p entry.definition
  result = entry.fasta(factory)
  result.each do |hit|
    print "#{hit.query_id} : #{hit.evalue}\t#{hit.target_id} at "
    p hit.lap_at
  end
end



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# File 'lib/bio/db/fasta.rb', line 186

def query(factory)
  factory.query(@entry)
end

#seq ⇒ Object

Returns a joined sequence line as a String.



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# File 'lib/bio/db/fasta.rb', line 193

def seq
  unless defined?(@seq)
    unless /\A\s*^\#/ =~ @data then
      @seq = Sequence::Generic.new(@data.tr(" \t\r\n0-9", '')) # lazy clean up
    else
      a = @data.split(/(^\#.*$)/)
      i = 0
      cmnt = {}
      s = []
      a.each do |x|
        if /^# ?(.*)$/ =~ x then
          cmnt[i] ? cmnt[i] << "\n" << $1 : cmnt[i] = $1
        else
          x.tr!(" \t\r\n0-9", '') # lazy clean up
          i += x.length
          s << x
        end
      end
      @comment = cmnt
      @seq = Bio::Sequence::Generic.new(s.join(''))
    end
  end
  @seq
end

#to_seq ⇒ Object

Returns sequence as a Bio::Sequence object.

Note: If you modify the returned Bio::Sequence object, the sequence or definition in this FastaFormat object might also be changed (but not always be changed) because of efficiency.



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# File 'lib/bio/db/fasta.rb', line 256

def to_seq
  seq
  obj = Bio::Sequence.new(@seq)
  obj.definition = self.definition
  obj
end