bio 2.0.3 → 2.0.5

data/lib/bio/db/embl/uniprotkb.rb

@@ -248,9 +248,8 @@ class UniProtKB < EMBLDB
   #  SYNONYM        >=0
   #  CONTEINS       >=0
   def protein_name
-    @data['DE'] ||= parse_DE_line_rel14(get('DE'))
-    parsed_de_line = @data['DE']
-    if parsed_de_line then
+    parsed_de_line = self.de
+    if parsed_de_line.kind_of?(Array) then
       # since UniProtKB release 14.0 of 22-Jul-2008
       name = nil
       parsed_de_line.each do |a|
@@ -275,7 +274,6 @@ class UniProtKB < EMBLDB
     return name
   end
 
-
   # returns synonyms (unofficial and/or alternative names).
   # Returns an Array containing String objects.
   #
@@ -292,9 +290,8 @@ class UniProtKB < EMBLDB
   # synonyms are each placed in () following the official name on the DE line.
   def synonyms
     ary = Array.new
-    @data['DE'] ||= parse_DE_line_rel14(get('DE'))
-    parsed_de_line = @data['DE']
-    if parsed_de_line then
+    parsed_de_line = self.de
+    if parsed_de_line.kind_of?(Array) then
       # since UniProtKB release 14.0 of 22-Jul-2008
       parsed_de_line.each do |a|
         case a[0]
@@ -330,6 +327,20 @@ class UniProtKB < EMBLDB
     return ary
   end
 
+  # Returns an Array (for new format since rel 14)
+  # or a String (for old format before rel 14) for the DE line.
+  #
+  def de
+    return @data['DE'] if @data['DE']
+    parsed_de_line = parse_DE_line_rel14(get('DE'))
+    case parsed_de_line
+    when Array # new format since rel14
+      @data['DE'] ||= parsed_de_line
+    else
+      super
+    end
+    @data['DE']
+  end
 
   # returns gene names in the GN line.
   #
@@ -519,22 +530,43 @@ class UniProtKB < EMBLDB
   # http://br.expasy.org/sprot/userman.html#OH_line
   def oh
     unless @data['OH']
-      @data['OH'] = fetch('OH').split("\. ").map {|x|
-        if x =~ /NCBI_TaxID=(\d+);/
-          taxid = $1
-        else
-          raise ArgumentError, ["Error: Invalid OH line format (#{self.entry_id}):",
-                                $!, "\n", get('OH'), "\n"].join
-          
-        end
-        if x =~ /NCBI_TaxID=\d+; (.+)/ 
-          host_name = $1
-          host_name.sub!(/\.$/, '')
-        else
-          host_name = nil
+      oh = []
+      a = fetch('OH').split(/(NCBI\_TaxID\=)(\d+)(\;)/)
+      t = catch :error do
+        taxid = nil
+        host_name = nil
+        while x = a.shift
+          x = x.to_s.strip
+          case x
+          when ''
+            next
+          when 'NCBI_TaxID='
+            if taxid then
+              oh.push({'NCBI_TaxID' => taxid, 'HostName' => host_name})
+              taxid = nil
+              host_name = nil
+            end
+            taxid = a.shift
+            throw :error, :missing_semicolon if a.shift != ';'
+          else
+            throw :error, :missing_taxid if host_name
+            host_name = x
+            host_name.sub!(/\.\z/, '')
+          end
+        end #while x...
+        if taxid then
+          oh.push({'NCBI_TaxID' => taxid, 'HostName' => host_name})
+        elsif host_name then
+          throw :error, :missing_taxid_last
         end
-        {'NCBI_TaxID' => taxid, 'HostName' => host_name}
-      }
+        nil
+      end #t = catch...
+      if t then
+        raise ArgumentError,
+              ["Error: Invalid OH line format (#{self.entry_id}):",
+               $!, "\n", get('OH'), "\n"].join
+      end
+      @data['OH'] = oh
     end
     @data['OH']
   end
@@ -911,6 +943,7 @@ class UniProtKB < EMBLDB
 
 
   def cc_alternative_products(data)
+    return nil unless data
     ap = data.join('')
     return ap unless ap
 
@@ -949,6 +982,7 @@ class UniProtKB < EMBLDB
 
 
   def cc_biophysiochemical_properties(data)
+    return nil unless data
     data = data[0]
 
     hash = {'Absorption' => {}, 
@@ -984,6 +1018,7 @@ class UniProtKB < EMBLDB
 
 
   def cc_caution(data)
+    return nil unless data
     data.join('')
   end
   private :cc_caution
@@ -993,6 +1028,7 @@ class UniProtKB < EMBLDB
   #
   #   CC       P46527:CDKN1B; NbExp=1; IntAct=EBI-359815, EBI-519280;
   def cc_interaction(data)
+    return nil unless data
     str = data.join('')
     it = str.scan(/(.+?); NbExp=(.+?); IntAct=(.+?);/)
     it.map {|ent|
@@ -1048,6 +1084,7 @@ class UniProtKB < EMBLDB
 
 
   def cc_pathway(data)
+    return nil unless data
     data.map {|x| x.sub(/\.$/, '') }.map {|x|
       x.split(/; | and |: /)
     }[0]
@@ -1056,6 +1093,7 @@ class UniProtKB < EMBLDB
 
 
   def cc_rna_editing(data)
+    return nil unless data
     data = data.join('')
     entry = {'Modified_positions' => [], 'Note' => ""}
     if data =~ /Modified_positions=(.+?)(\.|;)/
@@ -1072,6 +1110,7 @@ class UniProtKB < EMBLDB
 
 
   def cc_subcellular_location(data)
+    return nil unless data
     data.map {|x| 
       x.split('. ').map {|y| 
         y.split('; ').map {|z| 
@@ -1090,6 +1129,7 @@ class UniProtKB < EMBLDB
   #++
 
   def cc_web_resource(data)
+    return nil unless data
     data.map {|x|
       entry = {'Name' => nil, 'Note' => nil, 'URL' => nil}
       x.split(';').each do |y|
@@ -1197,9 +1237,128 @@ class UniProtKB < EMBLDB
     return ft[feature_key] if feature_key
     return @data['FT'] if @data['FT']
 
+    ftstr = get('FT')
+    ftlines = ftstr.split("\n")
+    for i in 0..10 do
+      if /^FT +([^\s]+) +(([^\s]+)\:)?([\<\?]?[0-9]+|\?)(?:\.\.([\>\?]?[0-9]+|\?))?\s*$/ =~ ftlines[i] &&
+         /^FT +\/([^\s\=]+)(?:\=(\")?(.+)(\")?)?\s*$/ =~ ftlines[i+1] then
+        fmt_2019_11 = true
+        break #for i
+      end
+    end #for i
+
+    hash = if fmt_2019_11 then
+             ft_2019_11_parser(ftlines)
+           else
+             ft_legacy_parser(ftlines)
+           end
+    @data['FT'] = hash
+  end
+
+  # FT parser since UniProt release 2019_11
+  # https://www.uniprot.org/release-notes/2019-12-18-release#text%5Fft
+  def ft_2019_11_parser(ftlines)
+    table = []
+    cur_ft = nil
+    cont = false
+    begin
+      ftlines.each do |line|
+        if /^FT +([^\s]+) +(([^\s]+)\:)?([\<\?]?[0-9]+|\?)(?:\.\.([\>\?]?[0-9]+|\?))?\s*$/ =~ line
+          f_name = $1.to_s
+          f_from = "#{$2}#{$4}"
+          f_to = $5.to_s
+          f_to = f_from if f_to.empty?
+          cur_ft = [f_name,   # Feature Name
+                    f_from,   # From
+                    f_to,     # To
+                    []        # Qualifiers
+                   ]
+          table.push cur_ft
+          cont = false
+        elsif cont && /^FT {19}/ =~ line
+          str = $'
+          str.rstrip!
+          orig = cur_ft[3][-1][1].to_s
+          if orig.size > 0 && orig[-1] != ' ' &&
+             str.length > 0 && str[0] != ' ' then
+            orig.concat ' '
+          end
+          orig.concat str
+          cur_ft[3][-1][1] = orig
+          if cont && orig[-1] == "\""
+            orig.chop!
+            cont = false
+          end
+        elsif /^FT +\/([^\s\=]+)(?:\=(\")?(.+))?\s*$/ =~ line
+          key = $1
+          val = $3
+          val.rstrip!
+          cur_ft[3].push [ key, val ]
+          cont = false
+          if $2 == "\""
+            if val.to_s[-1] == "\""
+              val.chop!
+            else
+              cont = true
+            end
+          end
+        else
+          raise "FT parse error: #{line.inspect}"
+        end
+      end
+
+      hash = {}
+      table.each do |feature|
+        cur_h = {
+          # Removing '<', '>' or '?' in FROM/TO endopoint.
+          'From' => feature[1].sub(/\D/, '').to_i,  
+          'To'   => feature[2].sub(/\D/, '').to_i, 
+          'diff' => [],
+          'original' => feature
+        }
+        hash[feature[0]] ||= []
+        hash[feature[0]].push cur_h
+        feature[3].each do |a|
+          case a[0]
+          when 'From', 'To', 'Description', 'FTId', 'diff', 'original'
+            ; # do nothing
+          else
+            cur_h[a[0]] = a[1]
+          end
+        end
+        if cur_h["id"] then
+          cur_h['FTId'] = cur_h['id']
+        end
+
+        case feature[0]
+        when 'VARSPLIC', 'VARIANT', 'VAR_SEQ', 'CONFLICT'
+          case cur_h['note'].to_s
+          when /(\w[\w ]*\w*) - ?> (\w[\w ]*\w*)/
+            original_res = $1
+            changed_res = $2
+            original_res = original_res.gsub(/ /,'').strip
+            chenged_res = changed_res.gsub(/ /,'').strip
+          when /Missing/i
+            original_res = seq.subseq(cur_h['From'],
+                                      cur_h['To'])
+            changed_res = ''
+          end
+          cur_h['diff'] = [original_res, chenged_res]
+        end
+      end
+    rescue
+      raise "Invalid FT Lines(#{$!}) in #{entry_id}:, \n'#{self.get('FT')}'\n"
+    end
+
+    hash
+  end
+  private :ft_2019_11_parser
+  
+  # FT parser for the format before Uniprot release 2019_11
+  def ft_legacy_parser(ftlines)
     table = []
     begin
-      get('FT').split("\n").each do |line|
+      ftlines.each do |line|
         if line =~ /^FT   \w/
           feature = line.chomp.ljust(74)
           table << [feature[ 5..12].strip,   # Feature Name
@@ -1256,10 +1415,9 @@ class UniProtKB < EMBLDB
       raise "Invalid FT Lines(#{$!}) in #{entry_id}:, \n'#{self.get('FT')}'\n"
     end
 
-    @data['FT'] = hash
+    hash
   end
-
-
+  private :ft_legacy_parser
 
   # returns a Hash of conteins in the SQ lines.
   # * Bio::UniProtKBL#sq  -> hsh

data/lib/bio/version.rb

@@ -10,7 +10,7 @@
 module Bio
 
   # BioRuby version (Array containing Integer)
-  BIORUBY_VERSION = [2, 0, 3].extend(Comparable).freeze
+  BIORUBY_VERSION = [2, 0, 5].extend(Comparable).freeze
 
   # Extra version specifier (String or nil).
   # Existance of the value indicates development version.

data/test/data/uniprot/P03589.uniprot

@@ -0,0 +1,127 @@
+ID   1A_AMVLE                Reviewed;        1126 AA.
+AC   P03589;
+DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
+DT   21-JUL-1986, sequence version 1.
+DT   22-FEB-2023, entry version 78.
+DE   RecName: Full=Replication protein 1a;
+DE   Includes:
+DE     RecName: Full=ATP-dependent helicase;
+DE              EC=3.6.4.-;
+DE   Includes:
+DE     RecName: Full=Methyltransferase;
+DE              EC=2.1.1.-;
+GN   ORFNames=ORF1a;
+OS   Alfalfa mosaic virus (strain 425 / isolate Leiden).
+OC   Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes;
+OC   Martellivirales; Bromoviridae; Alfamovirus.
+OX   NCBI_TaxID=12322;
+OH   NCBI_TaxID=4045; Apium graveolens (Celery).
+OH   NCBI_TaxID=83862; Astragalus glycyphyllos (Wild liquorice).
+OH   NCBI_TaxID=4072; Capsicum annuum (Capsicum pepper).
+OH   NCBI_TaxID=41386; Caryopteris incana.
+OH   NCBI_TaxID=3827; Cicer arietinum (Chickpea) (Garbanzo).
+OH   NCBI_TaxID=3847; Glycine max (Soybean) (Glycine hispida).
+OH   NCBI_TaxID=35936; Lablab purpureus (Hyacinth bean) (Dolichos lablab).
+OH   NCBI_TaxID=4236; Lactuca sativa (Garden lettuce).
+OH   NCBI_TaxID=3864; Lens culinaris (Lentil) (Cicer lens).
+OH   NCBI_TaxID=3869; Lupinus.
+OH   NCBI_TaxID=145753; Malva parviflora (Little mallow) (Cheeseweed mallow).
+OH   NCBI_TaxID=3879; Medicago sativa (Alfalfa).
+OH   NCBI_TaxID=4097; Nicotiana tabacum (Common tobacco).
+OH   NCBI_TaxID=3885; Phaseolus vulgaris (Kidney bean) (French bean).
+OH   NCBI_TaxID=23113; Philadelphus.
+OH   NCBI_TaxID=3888; Pisum sativum (Garden pea).
+OH   NCBI_TaxID=4081; Solanum lycopersicum (Tomato) (Lycopersicon esculentum).
+OH   NCBI_TaxID=4113; Solanum tuberosum (Potato).
+OH   NCBI_TaxID=157662; Teramnus repens.
+OH   NCBI_TaxID=60916; Trifolium incarnatum (Crimson clover).
+OH   NCBI_TaxID=85293; Viburnum opulus (High-bush cranberry).
+OH   NCBI_TaxID=3916; Vigna radiata var. radiata (Mung bean) (Phaseolus aureus).
+OH   NCBI_TaxID=3917; Vigna unguiculata (Cowpea).
+RN   [1]
+RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
+RX   PubMed=6298738; DOI=10.1093/nar/11.5.1253;
+RA   Cornelissen B.J.C., Brederode F.T., Moormann R.J.M., Bol J.F.;
+RT   "Complete nucleotide sequence of alfalfa mosaic virus RNA 1.";
+RL   Nucleic Acids Res. 11:1253-1265(1983).
+CC   -!- FUNCTION: Involved in the virus replication. Contains a helicase domain
+CC       and a methyltransferase domain. The methyltransferase domain is
+CC       probably involved in viral RNA capping. Involved in the formation of ER
+CC       membrane spherular invaginations in which RNA replication complexes
+CC       form (By similarity). {ECO:0000250}.
+CC   -!- SUBUNIT: Interacts with RNA-directed RNA polymerase 2a. {ECO:0000250}.
+CC   -!- SUBCELLULAR LOCATION: Host endoplasmic reticulum membrane
+CC       {ECO:0000250}; Peripheral membrane protein {ECO:0000250}.
+CC   -!- SIMILARITY: Belongs to the bromoviridae replication protein 1a family.
+CC       {ECO:0000305}.
+CC   ---------------------------------------------------------------------------
+CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
+CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
+CC   ---------------------------------------------------------------------------
+DR   EMBL; L00163; AAA46289.1; -; Genomic_RNA.
+DR   PIR; A04197; WMFM12.
+DR   RefSeq; NP_041192.1; NC_001495.1.
+DR   SMR; P03589; -.
+DR   GeneID; 962667; -.
+DR   KEGG; vg:962667; -.
+DR   Proteomes; UP000000358; Genome.
+DR   GO; GO:0044167; C:host cell endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
+DR   GO; GO:0016020; C:membrane; IEA:UniProtKB-KW.
+DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
+DR   GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
+DR   GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
+DR   GO; GO:0008174; F:mRNA methyltransferase activity; IEA:InterPro.
+DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
+DR   GO; GO:0006396; P:RNA processing; IEA:InterPro.
+DR   Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 2.
+DR   InterPro; IPR027351; (+)RNA_virus_helicase_core_dom.
+DR   InterPro; IPR002588; Alphavirus-like_MT_dom.
+DR   InterPro; IPR027417; P-loop_NTPase.
+DR   Pfam; PF01443; Viral_helicase1; 1.
+DR   Pfam; PF01660; Vmethyltransf; 1.
+DR   SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
+DR   PROSITE; PS51743; ALPHAVIRUS_MT; 1.
+DR   PROSITE; PS51657; PSRV_HELICASE; 1.
+PE   3: Inferred from homology;
+KW   ATP-binding; Helicase; Host endoplasmic reticulum; Host membrane;
+KW   Hydrolase; Membrane; Methyltransferase; Nucleotide-binding;
+KW   Reference proteome; Transferase.
+FT   CHAIN           1..1126
+FT                   /note="Replication protein 1a"
+FT                   /id="PRO_0000083254"
+FT   DOMAIN          90..278
+FT                   /note="Alphavirus-like MT"
+FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01079"
+FT   DOMAIN          806..963
+FT                   /note="(+)RNA virus helicase ATP-binding"
+FT   DOMAIN          964..1125
+FT                   /note="(+)RNA virus helicase C-terminal"
+FT   REGION          69..406
+FT                   /note="Methyltransferase"
+FT   REGION          834..1094
+FT                   /note="ATP-dependent helicase"
+FT   BINDING         838..845
+FT                   /ligand="ATP"
+FT                   /ligand_id="ChEBI:CHEBI:30616"
+FT                   /evidence="ECO:0000255"
+SQ   SEQUENCE   1126 AA;  125828 MW;  BF5A8019B47D4CBF CRC64;
+     MNADAQSTDA SLSMREPLSH ASIQEMLRRV VEKQAADDTT AIGKVFSEAG RAYAQDALPS
+     DKGEVLKISF SLDATQQNIL RANFPGRRTV FSNSSSSSHC FAAAHRLLET DFVYRCFGNT
+     VDSIIDLGGN FVSHMKVKRH NVHCCCPILD ARDGARLTER ILSLKSYVRK HPEIVGEADY
+     CMDTFQKCSR RADYAFAIHS TSDLDVGELA CSLDQKGVMK FICTMMVDAD MLIHNEGEIP
+     NFNVRWEIDR KKDLIHFDFI DEPNLGYSHR FSLLKHYLTY NAVDLGHAAY RIERKQDFGG
+     VMVIDLTYSL GFVPKMPHSN GRSCAWYNRV KGQMVVHTVN EGYYHHSYQT AVRRKVLVDK
+     KVLTRVTEVA FRQFRPNADA HSAIQSIATM LSSSTNHTII GGVTLISGKP LSPDDYIPVA
+     TTIYYRVKKL YNAIPEMLSL LDKGERLSTD AVLKGSEGPM WYSGPTFLSA LDKVNVPGDF
+     VAKALLSLPK RDLKSLFSRS ATSHSERTPV RDESPIRCTD GVFYPIRMLL KCLGSDKFES
+     VTITDPRSNT ETTVDLYQSF QKKIETVFSF ILGKIDGPSP LISDPVYFQS LEDVYYAEWH
+     QGNAIDASNY ARTLLDDIRK QKEESLKAKA KEVEDAQKLN RAILQVHAYL EAHPDGGKIE
+     GLGLSSQFIA KIPELAIPTP KPLPEFEKNA ETGEILRINP HSDAILEAID YLKSTSANSI
+     ITLNKLGDHC QWTTKGLDVV WAGDDKRRAF IPKKNTWVGP TARSYPLAKY ERAMSKDGYV
+     TLRWDGEVLD ANCVRSLSQY EIVFVDQSCV FASAEAIIPS LEKALGLEAH FSVTIVDGVA
+     GCGKTTNIKQ IARSSGRDVD LILTSNRSSA DELKETIDCS PLTKLHYIRT CDSYLMSASA
+     VKAQRLIFDE CFLQHAGLVY AAATLAGCSE VIGFGDTEQI PFVSRNPSFV FRHHKLTGKV
+     ERKLITWRSP ADATYCLEKY FYKNKKPVKT NSRVLRSIEV VPINSPVSVE RNTNALYLCH
+     TQAEKAVLKA QTHLKGCDNI FTTHEAQGKT FDNVYFCRLT RTSTSLATGR DPINGPCNGL
+     VALSRHKKTF KYFTIAHDSD DVIYNACRDA GNTDDSILAR SYNHNF
+//