Class | Bio::FastaDefline
In: | lib/bio/db/fasta/defline.rb
Parent: | Object

Parsing FASTA Defline, and extract IDs and other informations. IDs are NSIDs (NCBI standard FASTA sequence identifiers) or ":"-separated IDs.

specs are described in: ftp.ncbi.nih.gov/blast/documents/README.formatdb blast.wustl.edu/doc/FAQ-Indexing.html#Identifiers

### Examples

      rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
      rub.entry_id       ==> 'gi|671595'
      rub.get('emb')     ==> 'CAA85678.1'
      rub.emb            ==> 'CAA85678.1'
      rub.gi             ==> '671595'
      rub.accession      ==> 'CAA85678'
      rub.accessions     ==> [ 'CAA85678' ]
      rub.acc_version    ==> 'CAA85678.1'
      rub.locus          ==> nil
      rub.list_ids       ==> [["gi", "671595"],
                              ["emb", "CAA85678.1", nil],
                              ["Perovskia abrotanoides"]]

      ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
      ckr.entry_id      ==> "gi|2495000"
      ckr.sp            ==> "CCKR_CAVPO"
      ckr.pir           ==> "I51898"
      ckr.gb            ==> "AAB29504.1"
      ckr.gi            ==> "2495000"
      ckr.accession     ==> "AAB29504"
      ckr.accessions    ==> ["Q63931", "AAB29504"]
      ckr.acc_version   ==> "AAB29504.1"
      ckr.locus         ==> nil
      ckr.description   ==>
        "CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
      ckr.descriptions  ==>
        ["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
         "cholecystokinin A receptor - guinea pig",
         "cholecystokinin A receptor; CCK-A receptor [Cavia]"]
      ckr.words         ==>
        ["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
         "receptor", "type"]
      ckr.id_strings    ==>
        ["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
         "544724", "AAB29504.1", "Cavia"]
      ckr.list_ids      ==>
        [["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
         ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
         ["gb", "AAB29504.1", nil], ["Cavia"]]

### Refereneces

- Fasta format description (NCBI) www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
- Frequently Asked Questions: Indexing of Sequence Identifiers (by Warren R. Gish.) blast.wustl.edu/doc/FAQ-Indexing.html#Identifiers
- README.formatdb ftp.ncbi.nih.gov/blast/documents/README.formatdb

### Methods

acc_version accession accessions add_defline description descriptions get get_all_by_type get_by_type gi id_strings locus method_missing new to_s words

### Constants

NSIDs

=

{ # NCBI and WU-BLAST 'gi' => [ 'gi' ], # NCBI GI 'gb' => [ 'acc_version', 'locus' ], # GenBank 'emb' => [ 'acc_version', 'locus' ], # EMBL 'dbj' => [ 'acc_version', 'locus' ], # DDBJ 'sp' => [ 'accession', 'entry_id' ], # SWISS-PROT 'pdb' => [ 'entry_id', 'chain' ], # PDB 'bbs' => [ 'number' ], # GenInfo Backbone Id 'gnl' => [ 'database' , 'entry_id' ], # General database identifier 'ref' => [ 'acc_version' , 'locus' ], # NCBI Reference Sequence 'lcl' => [ 'entry_id' ], # Local Sequence identifier # WU-BLAST and NCBI 'pir' => [ 'accession', 'entry_id' ], # PIR 'prf' => [ 'accession', 'entry_id' ], # Protein Research Foundation 'pat' => [ 'country', 'number', 'serial' ], # Patents # WU-BLAST only 'bbm' => [ 'number' ], # NCBI GenInfo Backbone database identifier 'gim' => [ 'number' ], # NCBI GenInfo Import identifier 'gp' => [ 'acc_version', 'locus' ], # GenPept 'oth' => [ 'accession', 'name', 'release' ], # Other (user-definable) identifier 'tpd' => [ 'accession', 'name' ], # Third party annotation, DDBJ 'tpe' => [ 'accession', 'name' ], # Third party annotation, EMBL 'tpg' => [ 'accession', 'name' ], # Third party annotation, GenBank # Original 'ri' => [ 'entry_id', 'rearray_id', 'len' ], # RIKEN FANTOM DB }

KillWords

=

[ 'an', 'the', 'this', 'that', 'is', 'are', 'were', 'was', 'be', 'can', 'may', 'might', 'as', 'at', 'by', 'for', 'in', 'of', 'on', 'to', 'with', 'from', 'and', 'or', 'not', 'dna', 'rna', 'mrna', 'cdna', 'orf', 'aa', 'nt', 'pct', 'id', 'ec', 'sp', 'subsp', 'similar', 'involved', 'identical', 'identity', 'cds', 'clone', 'library', 'contig', 'contigs', 'homolog', 'homologue', 'homologs', 'homologous', 'protein', 'proteins', 'gene', 'genes', 'product', 'products', 'sequence', 'sequences', 'strain', 'strains', 'region', 'regions', ]

KillWordsHash | = | {}
KillRegexpArray | = | [ /\A\d{1,3}\%?\z/, /\A[A-Z][A-Za-z0-9\_]*[0-9]+[A-Za-z0-9\_]+\z/, /\A[A-Z][A-Z0-9]*\_[A-Z0-9\_]+\z/

### Attributes

entry_id | [R] | Shows a possibly unique identifier. Returns a string.
list_ids | [R] | Shows array that contains IDs (or ID-like strings). Returns an array of arrays of strings.

### Public Class methods

new(str)

Parses given string.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 176
    176:     def initialize(str)
    177:       @deflines = []
    178:       @info = {}
    179:       @list_ids = []
    180:
    181:       @entry_id = nil
    182:
    183:       lines = str.split("\x01")
    184:       lines.each do |line|
    185:         add_defline(line)
    186:       end
    187:     end

### Public Instance methods

acc_version()

Shows accession with version number. If the entry has more than two of such IDs, only the first ID are shown. Returns a string or nil.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 489
    489:     def acc_version
    490:       unless defined?(@acc_version) then
    491:         @acc_version = get_by_type('acc_version')
    492:       end
    493:       @acc_version
    494:     end

accession()

Shows an accession number.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 507
    507:     def accession
    508:       unless defined?(@accession) then
    509:         if acc_version then
    510:           @accession = acc_version.split('.')[0]
    511:         else
    512:           @accession = accessions[0]
    513:         end
    514:       end
    515:       @accession
    516:     end

accessions()

Shows accession numbers. Returns an array of strings.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 498
    498:     def accessions
    499:       unless defined?(@accessions) then
    500:         @accessions = get_all_by_type('accession', 'acc_version')
    501:         @accessions.collect! { |x| x.sub(/\..*\z/, '') }
    502:       end
    503:       @accessions
    504:     end

add_defline(str)

Parses given string and adds parsed data.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 190
    190:     def add_defline(str)
    191:       case str
    192:       when /^\>?\s*((?:[^\|\s]*\|)+[^\s]+)\s*(.*)$/
    193:         # NSIDs
    194:         # examples:
    195:         # >gi|9910844|sp|Q9UWG2|RL3_METVA 50S ribosomal protein L3P
    196:         #
    197:         # note: regexp (:?) means grouping without backreferences
    198:         i = $1
    199:         d = $2
    200:         tks = i.split('|')
    201:         tks << '' if i[-1,1] == '|'
    202:         a = parse_NSIDs(tks)
    203:         i = a[0].join('|')
    204:         a.unshift('|')
    205:         d = tks.join('|') + ' ' + d unless tks.empty?
    206:         a << d
    207:         this_line = a
    208:         match_EC(d)
    209:         parse_square_brackets(d).each do |x|
    210:           if !match_EC(x, false) and x =~ /\A[A-Z]/ then
    211:             di = [  x ]
    212:             @list_ids << di
    213:             @info['organism'] = x unless @info['organism']
    214:           end
    215:         end
    216:
    217:       when /^\>?\s*([a-zA-Z0-9]+\:[^\s]+)\s*(.*)$/
    218:         # examples:
    219:         # >sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
    220:         # >emb:CACDC28 [X80034] C.albicans CDC28 gene
    221:         i = $1
    222:         d = $2
    223:         a = parse_ColonSepID(i)
    224:         i = a.join(':')
    225:         this_line = [ ':', a , d ]
    226:         match_EC(d)
    227:         parse_square_brackets(d).each do |x|
    228:           if !match_EC(x, false) and x =~ /:/ then
    229:             parse_ColonSepID(x)
    230:           elsif x =~ /\A\s*([A-Z][A-Z0-9_\.]+)\s*\z/ then
    231:             @list_ids << [ $1 ]
    232:           end
    233:         end
    234:
    235:       when /^\>?\s*(\S+)(?:\s+(.+))?$/
    236:         # examples:
    237:         # >ABC12345 this is test
    238:         i = $1
    239:         d = $2.to_s
    240:         @list_ids << [ i.chomp('.') ]
    241:         this_line = [  '', [ i ], d ]
    242:         match_EC(d)
    243:       else
    244:         i = str
    245:         d = ''
    246:         match_EC(i)
    247:         this_line = [ '', [ i ], d ]
    248:       end
    249:
    250:       @deflines << this_line
    251:       @entry_id = i unless @entry_id
    252:     end

description()

Shows description.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 332
    332:     def description
    333:       @deflines[0].to_a[-1]
    334:     end

descriptions()

Returns descriptions.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 337
    337:     def descriptions
    338:       @deflines.collect do |a|
    339:         a[-1]
    340:       end
    341:     end

get(dbname)

Returns identifires by a database name.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 413
    413:     def get(dbname)
    414:       db = dbname.to_s
    415:       r = nil
    416:       unless r = @info[db] then
    417:         di = @list_ids.find { |x| x[0] == db.to_s }
    418:         if di and di.size <= 2 then
    419:           r = di[-1]
    420:         elsif di then
    421:           labels = self.class::NSIDs[db]
    422:           [ 'acc_version', 'entry_id',
    423:             'locus', 'accession', 'number'].each do |x|
    424:             if i = labels.index(x) then
    425:               r = di[i+1]
    426:               break if r
    427:             end
    428:           end
    429:           r = di[1..-1].find { |x| x } unless r
    430:         end
    431:         @info[db] = r if r
    432:       end
    433:       r
    434:     end

get_all_by_type(*type_strarg)

Returns identifiers by given type.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 449
    449:     def get_all_by_type(*type_strarg)
    450:       d = []
    451:       @list_ids.each do |x|
    452:         if labels = self.class::NSIDs[x[0]] then
    453:           type_strarg.each do |y|
    454:             if i = labels.index(y) then
    455:               d << x[i+1] if x[i+1]
    456:             end
    457:           end
    458:         end
    459:       end
    460:       d
    461:     end

get_by_type(type_str)

Returns an identifier by given type.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 437
    437:     def get_by_type(type_str)
    438:       @list_ids.each do |x|
    439:         if labels = self.class::NSIDs[x[0]] then
    440:           if i = labels.index(type_str) then
    441:             return x[i+1]
    442:           end
    443:         end
    444:       end
    445:       nil
    446:     end

gi()

Shows GI. If the entry has more than two of such IDs, only the first ID are shown. Returns a string or nil.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 478
    478:     def gi
    479:       unless defined?(@gi) then
    480:         @gi = get_by_type('gi')
    481:       end
    482:       @gi
    483:     end

id_strings()

Shows ID-like strings. Returns an array of strings.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 345
    345:     def id_strings
    346:       r = []
    347:       @list_ids.each do |a|
    348:         if a.size >= 2 then
    349:           r.concat a[1..-1].find_all { |x| x }
    350:         else
    351:           if a[0].to_s.size > 0 and a[0] =~ /\A[A-Za-z0-9\.\-\_]+\z/
    352:             r << a[0]
    353:           end
    354:         end
    355:       end
    356:       r.concat( words(true, []).find_all do |x|
    357:                  x =~ /\A[A-Z][A-Za-z0-9\_]*[0-9]+[A-Za-z0-9\_]+\z/ or
    358:                    x =~ /\A[A-Z][A-Z0-9]*\_[A-Z0-9\_]+\z/
    359:                end)
    360:       r
    361:     end

locus()

Shows locus. If the entry has more than two of such IDs, only the first ID are shown. Returns a string or nil.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 467
    467:     def locus
    468:       unless defined?(@locus)
    469:         @locus = get_by_type('locus')
    470:       end
    471:       @locus
    472:     end

method_missing(name, *args)

[Source]

         # File lib/bio/db/fasta/defline.rb, line 518
    518:     def method_missing(name, *args)
    519:       # raise ArgumentError,
    520:       # "wrong # of arguments(#{args.size} for 1)" if args.size >= 2
    521:       r = get(name, *args)
    522:       if !r and !(self.class::NSIDs[name.to_s]) then
    523:         raise "NameError: undefined method `#{name.inspect}'"
    524:       end
    525:       r
    526:     end

to_s()

Shows original string. Note that the result of this method may be different from original string which is given in FastaDefline.new method.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 324
    324:     def to_s
    325:       @deflines.collect { |a|
    326:         s = a[0]
    327:         (a[1..-2].collect { |x| x.join(s) }.join(s) + ' ' + a[-1]).strip
    328:       }.join("\x01")
    329:     end

words(case_sensitive = nil, kill_regexp = self.class::KillRegexpArray, kwhash = self.class::KillWordsHash)

Shows words used in the defline. Returns an Array.

[Source]

         # File lib/bio/db/fasta/defline.rb, line 387
    387:     def words(case_sensitive = nil, kill_regexp = self.class::KillRegexpArray,
    388:               kwhash = self.class::KillWordsHash)
    389:       a = descriptions.join(' ').split(/[\.\,\;\:\(\)\[\]\{\}\<\>\"\'\`\~\/\|\?\!\&\@\#\s\x00-\x1f\x7f]+/)
    390:       a.collect! do |x|
    391:         x.sub!(/\A[\$\*\-\+]+/, '')
    392:         x.sub!(/[\$\*\-\=]+\z/, '')
    393:         if x.size <= 1 then
    394:           nil
    395:         elsif kwhash[x.downcase] then
    396:           nil
    397:         else
    398:           if kill_regexp.find { |expr| expr =~ x } then
    399:             nil
    400:           else
    401:             x
    402:           end
    403:         end
    404:       end
    405:       a.compact!
    406:       a.collect! { |x| x.downcase } unless case_sensitive
    407:       a.sort!
    408:       a.uniq!
    409:       a
    410:     end

[Validate]