Class | Bio::NBRF
In: | lib/bio/db/nbrf.rb
Parent: | DB

Sequence data class for NBRF/PIR flatfile format.

### Methods

aalen aaseq entry length nalen naseq new seq seq_class to_nbrf to_s

### Constants

DELIMITER | = | RS = "\n>" |  | Delimiter of each entry. Bio::FlatFile uses it.
DELIMITER_OVERRUN | = | 1 |  | (Integer) excess read size included in DELIMITER.

### External Aliases

entry_id | -> | accession

### Attributes

data | [RW] | sequence data of the entry (???)
definition | [RW] | Returns the description line of the NBRF/PIR formatted data.
entry_id | [RW] | Returns ID described in the entry.
entry_overrun | [R] | piece of next entry. Bio::FlatFile uses it.
seq_type | [RW] | 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)

### Public Class methods

new(str)

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.

[Source]

        # File lib/bio/db/nbrf.rb, line 45
    45:     def initialize(str)
    46:       str = str.sub(/\A[\r\n]+/, '') # remove first void lines
    47:       line1, line2, rest = str.split(/^/, 3)
    48:
    49:       rest = rest.to_s
    50:       rest.sub!(/^>.*/m, '') # remove trailing entries for sure
    51:       @entry_overrun = $&
    52:       rest.sub!(/\*\s*\z/, '') # remove last '*' and "\n"
    53:       @data = rest
    54:
    55:       @definition = line2.to_s.chomp
    56:       if /^>?([A-Za-z0-9]{2})\;(.*)/ =~ line1.to_s then
    57:         @seq_type = $1
    58:         @entry_id = $2
    59:       end
    60:     end

to_nbrf(hash)

Creates a NBRF/PIR formatted text. Parameters can be omitted.

[Source]

         # File lib/bio/db/nbrf.rb, line 167
    167:     def self.to_nbrf(hash)
    168:       seq_type = hash[:seq_type]
    169:       seq = hash[:seq]
    170:       unless seq_type
    171:         if seq.is_a?(Bio::Sequence::AA) then
    172:           seq_type = 'P1'
    173:         elsif seq.is_a?(Bio::Sequence::NA) then
    174:           seq_type = /u/i =~ seq ? 'RL' : 'DL'
    175:         else
    176:           seq_type = 'XX'
    177:         end
    178:       end
    179:       width = hash.has_key?(:width) ? hash[:width] : 70
    180:       if width then
    181:         seq = seq.to_s + "*"
    182:         seq.gsub!(Regexp.new(".{1,#{width}}"), "\\0\n")
    183:       else
    184:         seq = seq.to_s + "*\n"
    185:       end
    186:       ">#{seq_type};#{hash[:entry_id]}\n#{hash[:definition]}\n#{seq}"
    187:     end

### Public Instance methods

aalen()

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.

[Source]

         # File lib/bio/db/nbrf.rb, line 157
    157:     def aalen
    158:       aaseq.length
    159:     end

aaseq()

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.

[Source]

         # File lib/bio/db/nbrf.rb, line 143
    143:     def aaseq
    144:       if seq.is_a?(Bio::Sequence::NA) then
    145:         raise 'not nucleic but protein sequence'
    146:       elsif seq.is_a?(Bio::Sequence::AA) then
    147:         seq
    148:       else
    149:         Bio::Sequence::AA.new(seq)
    150:       end
    151:     end

entry()

Returns the stored one entry as a NBRF/PIR format. (same as to_s)

[Source]

        # File lib/bio/db/nbrf.rb, line 84
    84:     def entry
    85:       @entry = ">#{@seq_type or 'XX'};#{@entry_id}\n#{definition}\n#{@data}*\n"
    86:     end

length()

Returns sequence length.

[Source]

         # File lib/bio/db/nbrf.rb, line 115
    115:     def length
    116:       seq.length
    117:     end

nalen()

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.

[Source]

         # File lib/bio/db/nbrf.rb, line 135
    135:     def nalen
    136:       naseq.length
    137:     end

naseq()

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.

[Source]

         # File lib/bio/db/nbrf.rb, line 122
    122:     def naseq
    123:       if seq.is_a?(Bio::Sequence::AA) then
    124:         raise 'not nucleic but protein sequence'
    125:       elsif seq.is_a?(Bio::Sequence::NA) then
    126:         seq
    127:       else
    128:         Bio::Sequence::NA.new(seq)
    129:       end
    130:     end

seq()

Returns sequence data. Returns Bio::Sequence::NA, Bio::Sequence::AA or Bio::Sequence, according to the sequence type.

[Source]

         # File lib/bio/db/nbrf.rb, line 107
    107:     def seq
    108:       unless defined?(@seq)
    109:         @seq = seq_class.new(@data.tr(" \t\r\n0-9", '')) # lazy clean up
    110:       end
    111:       @seq
    112:     end

seq_class()

Returns Bio::Sequence::AA, Bio::Sequence::NA, or Bio::Sequence, depending on sequence type.

[Source]

         # File lib/bio/db/nbrf.rb, line 91
     91:     def seq_class
     92:       case @seq_type
     93:       when /[PF]1/
     94:         # protein
     95:         Sequence::AA
     96:       when /[DR][LC]/, /N[13]/
     97:         # nucleic
     98:         Sequence::NA
     99:       else
    100:         Sequence
    101:       end
    102:     end

to_s()

Alias for entry

[Validate]