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                    <== definition line
ATGCATGCATGCATGCATGCATGCATGCATGCATGC        <== sequence lines
ATGCATGCATGCATGCATGCATGCATGCATGCATGC
ATGCATGCATGC

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

Examples

fasta_string = <<END_OF_STRING
>gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c]
MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNI
VRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQ
NLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKP
IFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDP
INRISARRAAIHPYFQES
END_OF_STRING

f = Bio::FastaFormat.new(fasta_string)

f.entry #=> ">gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c]\n"+
# MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNI\n"+
# VRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQ\n"+
# NLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKP\n"+
# IFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDP\n"+
# INRISARRAAIHPYFQES"

Methods related to the name of the sequence

A larger range of methods for dealing with Fasta definition lines can be found in FastaDefline, accessed through the FastaFormat#identifiers method.

f.entry_id #=> "gi|398365175"
f.first_name #=> "gi|398365175|ref|NP_009718.3|"
f.definition #=> "gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c]"
f.identifiers #=> Bio::FastaDefline instance
f.accession #=> "NP_009718"
f.accessions #=> ["NP_009718"]
f.acc_version #=> "NP_009718.3"
f.comment #=> nil

Methods related to the actual sequence

f.seq #=> "MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES"
f.data #=> "\nMSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNI\nVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQ\nNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKP\nIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDP\nINRISARRAAIHPYFQES\n"
f.length #=> 298
f.aaseq #=> "MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES"
f.aaseq.composition #=> {"M"=>5, "S"=>15, "G"=>21, "E"=>16, "L"=>36, "A"=>17, "N"=>8, "Y"=>13, "K"=>22, "R"=>20, "V"=>18, "T"=>7, "D"=>23, "P"=>17, "Q"=>10, "I"=>23, "H"=>7, "F"=>12, "C"=>4, "W"=>4}
f.aalen #=> 298

A less structured fasta entry

f.entry #=> ">abc 123 456\nASDF"

f.entry_id #=> "abc"
f.first_name #=> "abc"
f.definition #=> "abc 123 456"
f.comment #=> nil
f.accession #=> nil
f.accessions #=> []
f.acc_version #=> nil

f.seq #=> "ASDF"
f.data #=> "\nASDF\n"
f.length #=> 4
f.aaseq #=> "ASDF"
f.aaseq.composition #=> {"A"=>1, "S"=>1, "D"=>1, "F"=>1}
f.aalen #=> 4

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 133

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

#dataObject

The seuqnce lines in text.


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# File 'lib/bio/db/fasta.rb', line 126

def data
  @data
end

#definitionObject

The comment line of the FASTA formatted data.


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# File 'lib/bio/db/fasta.rb', line 123

def definition
  @definition
end

#entry_overrunObject (readonly)

Returns the value of attribute entry_overrun


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# File 'lib/bio/db/fasta.rb', line 128

def entry_overrun
  @entry_overrun
end

Instance Method Details

#aalenObject

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


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# File 'lib/bio/db/fasta.rb', line 223

def aalen
  self.aaseq.length
end

#aaseqObject

Returens the Bio::Sequence::AA.


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# File 'lib/bio/db/fasta.rb', line 218

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

#acc_versionObject

Returns accession number with version.


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# File 'lib/bio/db/fasta.rb', line 279

def acc_version
  identifiers.acc_version
end

#accessionObject

Returns an accession number.


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

def accession
  identifiers.accession
end

#accessionsObject

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 274

def accessions
  identifiers.accessions
end

#commentObject

Returns comments.


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# File 'lib/bio/db/fasta.rb', line 197

def comment
  seq
  @comment
end

#entryObject 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 141

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

#entry_idObject

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 253

def entry_id
  identifiers.entry_id
end

#first_nameObject

Returns the first name (word) of the definition line - everything before the first whitespace.

>abc def #=> 'abc'
>gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c] #=> 'gi|398365175|ref|NP_009718.3|'
>abc #=> 'abc'

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# File 'lib/bio/db/fasta.rb', line 294

def first_name
  index = definition.index(/\s/)
  if index.nil?
    return @definition
  else
    return @definition[0...index]
  end
end

#giObject

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 262

def gi
  identifiers.gi
end

#identifiersObject

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 243

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

#lengthObject

Returns sequence length.


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# File 'lib/bio/db/fasta.rb', line 203

def length
  seq.length
end

#locusObject

Returns locus.


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# File 'lib/bio/db/fasta.rb', line 284

def locus
  identifiers.locus
end

#nalenObject

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


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# File 'lib/bio/db/fasta.rb', line 213

def nalen
  self.naseq.length
end

#naseqObject

Returens the Bio::Sequence::NA.


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# File 'lib/bio/db/fasta.rb', line 208

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 164

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

#seqObject

Returns a joined sequence line as a String.


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# File 'lib/bio/db/fasta.rb', line 171

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_biosequenceObject Also known as: to_seq

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 234

def to_biosequence
  Bio::Sequence.adapter(self, Bio::Sequence::Adapter::FastaFormat)
end