[BioRuby-cvs] bioruby/lib/bio/db nbrf.rb,1.4,1.5
Naohisa Goto
ngoto at pub.open-bio.org
Mon Oct 31 18:58:22 EST 2005
Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv5654
Modified Files:
nbrf.rb
Log Message:
changed document from RD to RDoc.
Index: nbrf.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/nbrf.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** nbrf.rb 26 Sep 2005 13:00:06 -0000 1.4
--- nbrf.rb 31 Oct 2005 23:58:19 -0000 1.5
***************
*** 1,8 ****
#
! # bio/db/nbrf.rb - NBRF/PIR format sequence data class
#
! # Copyright (C) 2001-2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # Copyright (C) 2001-2002 KATAYAMA Toshiaki <k at bioruby.org>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
--- 1,10 ----
#
! # = bio/db/nbrf.rb - NBRF/PIR format sequence data class
#
! # Copyright:: Copyright (C) 2001-2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # Copyright (C) 2001-2002 KATAYAMA Toshiaki <k at bioruby.org>
! # Licence:: LGPL
#
+ #--
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
***************
*** 18,34 ****
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id$
#
require 'bio/db'
require 'bio/sequence'
! module Bio
class NBRF < DB
# based on Bio::FastaFormat class
DELIMITER = RS = "*\n"
def initialize(str)
str = str.sub(/\A[\r\n]+/, '') # remove first void lines
--- 20,53 ----
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ #++
#
# $Id$
#
+ # 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'
! # Sequence data class for NBRF/PIR flatfile format.
! module Bio #:nodoc:
class NBRF < DB
+ #--
# based on Bio::FastaFormat class
+ #++
+ # Delimiter of each entry. Bio::FlatFile uses it.
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
***************
*** 47,55 ****
end
end
- attr_accessor :seq_type, :entry_id, :definition, :data
- attr_reader :entry_overrun
alias accession entry_id
def entry
@entry = ">#{@seq_type or 'XX'};#{@entry_id}\n#{definition}\n#{@data}*\n"
--- 66,92 ----
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"
***************
*** 57,60 ****
--- 94,99 ----
alias to_s entry
+ # Returns Bio::Sequence::AA, Bio::Sequence::NA, or Bio::Sequence,
+ # depending on sequence type.
def seq_class
case @seq_type
***************
*** 70,73 ****
--- 109,115 ----
end
+ # Returns sequence data.
+ # Returns Bio::Sequence::NA, Bio::Sequence::AA or Bio::Sequence,
+ # according to the sequence type.
def seq
unless defined?(@seq)
***************
*** 77,84 ****
--- 119,130 ----
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
***************
*** 91,98 ****
--- 137,151 ----
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
***************
*** 105,113 ****
--- 158,175 ----
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]
***************
*** 134,218 ****
end #class NBRF
end #module Bio
-
- =begin
-
- = Bio::NBRF
-
- This is a sequence data class for NBRF/PIR flatfile format.
-
- 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
-
- The precedent '>' can be omitted and the trailing '>' will be removed
- automatically.
-
- --- Bio::NBRF.new(entry)
-
- 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.
-
- --- Bio::NBRF#entry
-
- Returns the stored one entry as a NBRF/PIR format. (same as to_s)
-
-
- --- Bio::NBRF#seq_type
-
- 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)
-
- --- Bio::NBRF#seq_class
-
- Returns Bio::Sequence::AA, Bio::Sequence::NA, or Bio::Sequence,
- depending on sequence type.
-
- --- Bio::NBRF#entry_id
-
- Returns ID described in the entry.
-
- --- Bio::NBRF#accession
-
- Same as Bio::NBRF#entry_id.
-
- --- Bio::NBRF#definition
-
- Returns the description line of the NBRF/PIR formatted data.
-
- --- Bio::NBRF#seq
-
- Returns a joined sequence line as a String.
- Returns Bio::Sequence::NA, Bio::Sequence::AA or Bio::Sequence,
- according to the sequence type.
-
- --- Bio::NBRF#length
-
- Returns sequence length.
-
- --- Bio::NBRF#naseq
- --- Bio::NBRF#nalen
- --- Bio::NBRF#aaseq
- --- Bio::NBRF#aalen
-
- If you know whether the sequence is NA or AA, use these methods.
- 'naseq' and 'aaseq' methods returen the Bio::Sequence::NA or
- Bio::Sequence::AA object respectively. 'nalen' and 'aalen' methods
- return the length of them.
-
- If you call naseq for protein sequence, or aaseq for nucleic sequence,
- a RuntimeError will be occurred.
-
- --- Bio::NBRF.to_nbrf(:seq_type=>'P1', :entry_id=>'XXX00000',
- :definition=>'xxx protein',
- :seq=>seq, :width=>70)
-
- Creates a NBRF/PIR formatted text.
- Parameters can be omitted.
-
- =end
--- 196,198 ----
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