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|
#
# = bio/db/nbrf.rb - NBRF/PIR format sequence data class
#
# Copyright:: Copyright (C) 2001-2003,2006 Naohisa Goto <ng@bioruby.org>
# Copyright (C) 2001-2002 Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id: nbrf.rb,v 1.10 2007/04/05 23:35:40 trevor Exp $
#
# Sequence data class for NBRF/PIR flatfile format.
#
# = References
#
# * http://pir.georgetown.edu/pirwww/otherinfo/doc/techbulletin.html
# * http://www.sander.embl-ebi.ac.uk/Services/webin/help/webin-align/align_format_help.html#pir
# * http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html
#
require 'bio/db'
require 'bio/sequence'
module Bio
# Sequence data class for NBRF/PIR flatfile format.
class NBRF < DB
#--
# based on Bio::FastaFormat class
#++
# Delimiter of each entry. Bio::FlatFile uses it.
DELIMITER = RS = "\n>"
# (Integer) excess read size included in DELIMITER.
DELIMITER_OVERRUN = 1 # '>'
#--
# Note: DELIMITER is changed due to the change of Bio::FlatFile.
# DELIMITER = RS = "*\n"
#++
# Creates a new NBRF object. It stores the comment and sequence
# information from one entry of the NBRF/PIR format string.
# If the argument contains more than one
# entry, only the first entry is used.
def initialize(str)
str = str.sub(/\A[\r\n]+/, '') # remove first void lines
line1, line2, rest = str.split(/^/, 3)
rest = rest.to_s
rest.sub!(/^>.*/m, '') # remove trailing entries for sure
@entry_overrun = $&
rest.sub!(/\*\s*\z/, '') # remove last '*' and "\n"
@data = rest
@definition = line2.to_s.chomp
if /^>?([A-Za-z0-9]{2})\;(.*)/ =~ line1.to_s then
@seq_type = $1
@entry_id = $2
end
end
# Returns sequence type described in the entry.
# P1 (protein), F1 (protein fragment)
# DL (DNA linear), DC (DNA circular)
# RL (DNA linear), RC (DNA circular)
# N3 (tRNA), N1 (other functional RNA)
attr_accessor :seq_type
# Returns ID described in the entry.
attr_accessor :entry_id
alias accession entry_id
# Returns the description line of the NBRF/PIR formatted data.
attr_accessor :definition
# sequence data of the entry (???)
attr_accessor :data
# piece of next entry. Bio::FlatFile uses it.
attr_reader :entry_overrun
# Returns the stored one entry as a NBRF/PIR format. (same as to_s)
def entry
@entry = ">#{@seq_type or 'XX'};#{@entry_id}\n#{definition}\n#{@data}*\n"
end
alias to_s entry
# Returns Bio::Sequence::AA, Bio::Sequence::NA, or Bio::Sequence,
# depending on sequence type.
def seq_class
case @seq_type
when /[PF]1/
# protein
Sequence::AA
when /[DR][LC]/, /N[13]/
# nucleic
Sequence::NA
else
Sequence
end
end
# Returns sequence data.
# Returns Bio::Sequence::NA, Bio::Sequence::AA or Bio::Sequence,
# according to the sequence type.
def seq
unless defined?(@seq)
@seq = seq_class.new(@data.tr(" \t\r\n0-9", '')) # lazy clean up
end
@seq
end
# Returns sequence length.
def length
seq.length
end
# Returens the nucleic acid sequence.
# If you call naseq for protein sequence, RuntimeError will be occurred.
# Use the method if you know whether the sequence is NA or AA.
def naseq
if seq.is_a?(Bio::Sequence::AA) then
raise 'not nucleic but protein sequence'
elsif seq.is_a?(Bio::Sequence::NA) then
seq
else
Bio::Sequence::NA.new(seq)
end
end
# Returens the length of sequence.
# If you call nalen for protein sequence, RuntimeError will be occurred.
# Use the method if you know whether the sequence is NA or AA.
def nalen
naseq.length
end
# Returens the protein (amino acids) sequence.
# If you call aaseq for nucleic acids sequence,
# RuntimeError will be occurred.
# Use the method if you know whether the sequence is NA or AA.
def aaseq
if seq.is_a?(Bio::Sequence::NA) then
raise 'not nucleic but protein sequence'
elsif seq.is_a?(Bio::Sequence::AA) then
seq
else
Bio::Sequence::AA.new(seq)
end
end
# Returens the length of protein (amino acids) sequence.
# If you call aaseq for nucleic acids sequence,
# RuntimeError will be occurred.
# Use the method if you know whether the sequence is NA or AA.
def aalen
aaseq.length
end
#--
#class method
#++
# Creates a NBRF/PIR formatted text.
# Parameters can be omitted.
def self.to_nbrf(hash)
seq_type = hash[:seq_type]
seq = hash[:seq]
unless seq_type
if seq.is_a?(Bio::Sequence::AA) then
seq_type = 'P1'
elsif seq.is_a?(Bio::Sequence::NA) then
seq_type = /u/i =~ seq ? 'RL' : 'DL'
else
seq_type = 'XX'
end
end
width = hash.has_key?(:width) ? hash[:width] : 70
if width then
seq = seq.to_s + "*"
seq.gsub!(Regexp.new(".{1,#{width}}"), "\\0\n")
else
seq = seq.to_s + "*\n"
end
">#{seq_type};#{hash[:entry_id]}\n#{hash[:definition]}\n#{seq}"
end
end #class NBRF
end #module Bio
|
