Class: Bio::EuPathDB::FastaParser

Inherits:
Object
  • Object
show all
Defined in:
lib/eupathdb_fasta.rb

Overview

Looks like EuPathDB databases have settled on something like >gb|TGME49_000380 | organism=Toxoplasma_gondii_ME49 | product=myb-like DNA binding domain-containing protein | location=TGME49_chrVIII:6835359-6840923(-) | length=1528 where the species name differs but the rest is mostly constant

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(species_name, filename) ⇒ FastaParser

The species name is what should show up in the 2nd bracket, so something like ‘Toxoplasma_gondii_ME49’ for >gb|TGME49_000380 | organism=Toxoplasma_gondii_ME49 | product=myb-like DNA binding domain-containing protein | location=TGME49_chrVIII:6835359-6840923(-) | length=1528 for instance



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# File 'lib/eupathdb_fasta.rb', line 15

def initialize(species_name, filename)
  @species_name = species_name
  @filename = filename
end

Instance Attribute Details

#species_name ⇒ Object

Returns the value of attribute species_name.



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# File 'lib/eupathdb_fasta.rb', line 9

def species_name
  @species_name
end

Instance Method Details

#each ⇒ Object

Enumerate through fasta file entries



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# File 'lib/eupathdb_fasta.rb', line 21

def each
  @flat = Bio::FlatFile.open(Bio::FastaFormat, @filename)
  n = next_entry
  while !n.nil?
    yield n
    n = next_entry
  end
end

#next_entry ⇒ Object

Return the entry in the fasta file, or nil if there is no more or the fasta file could not be opened correctly.



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# File 'lib/eupathdb_fasta.rb', line 32

def next_entry
  return nil if !@flat
  n = @flat.next_entry
  return nil if !n
  
  s = parse_name(n.definition)
  s.sequence = n.seq
  return s
end

#parse_name(definition) ⇒ Object 



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# File 'lib/eupathdb_fasta.rb', line 42

def parse_name(definition)
  s = FastaAnnotation.new
  
  regex = /^(\S+)\|(.*?) \| organism=#{@species_name} \| product=(.*?) \| location=(.*) \| length=\d+$/
  matches = definition.match(regex)
  
  if !matches
    raise Exception, "Definition line has unexpected format: `#{definition}'. Trying to match this line to the regular expression `#{regex.inspect}'"
  end
  
  matches2 = matches[4].match(/^(.+?)\:/)
  if !matches2
    raise ParseException, "Definition line has unexpected scaffold format: #{matches[4]}"
  end
  s.sequencing_centre = matches[1]
  s.scaffold = matches2[1]
  s.gene_id = matches[2]
  s.annotation = matches[3]
  return s
end