Formating

doc/sphinx/source/embl.rst

@@ -14,6 +14,8 @@ The ENA flat-file format
 The entries in the database are structured so as to be usable by human readers as well as by computer programs. The explanations, descriptions, classifications and other comments are in ordinary English, and the symbols and formatting employed for the base sequences themselves have been chosen for readability. Wherever possible, symbols familiar to molecular biologists have been used. At the same time, the structure is systematic enough to allow computer programs easily to read, identify, and manipulate the various types of data included. Each entry in the database is composed of lines. Different types of lines, each with its own format, are used to record the various types of data which make up the entry. In general, fixed format items have been kept to a minimum, and a more syntax-oriented structure adopted for the lines. The two exceptions to this are the sequence data lines and the feature table lines, for which a fixed format was felt to offer significant advantages to the user. Users who write programs to process the database entries should not make any assumptions about the column placement of items on lines other than these two: all other line types are free-format. 
 
 Note that each line begins with a two-character line code, which indicates the type of information contained in the line. The currently used line types, along with their respective line codes, are listed below:
+
+==================================== =================================
      ID - identification             (begins each entry; 1 per entry)
      AC - accession number           (>=1 per entry)
      PR - project identifier         (0 or 1 per entry)
@@ -42,107 +44,110 @@ Note that each line begins with a two-character line code, which indicates the t
      CO - contig/construct line      (0 or >=1 per entry) 
      bb - (blanks) sequence data     (>=1 per entry)
      // - termination line           (ends each entry; 1 per entry)
+==================================== =================================
      
 Note that some entries will not contain all of the line types, and some line types occur many times in a single entry. As indicated, each entry begins with an identification line (ID) and ends with a terminator line (//). The various line types appear in entries in the order in which they are listed above (except for XX lines which may appear anywhere between the ID and SQ lines). A detailed description of each line type is given in the following sections.
 
-ID   X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP.
-XX
-AC   X56734; S46826;
-XX
-DT   12-SEP-1991 (Rel. 29, Created)
-DT   25-NOV-2005 (Rel. 85, Last updated, Version 11)
-XX
-DE   Trifolium repens mRNA for non-cyanogenic beta-glucosidase
-XX
-KW   beta-glucosidase.
-XX
-OS   Trifolium repens (white clover)
-OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
-OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
-OC   fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium.
-XX
-RN   [5]
-RP   1-1859
-RX   DOI; 10.1007/BF00039495.
-RX   PUBMED; 1907511.
-RA   Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
-RT   "Nucleotide and derived amino acid sequence of the cyanogenic
-RT   beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
-RL   Plant Mol. Biol. 17(2):209-219(1991).
-XX
-RN   [6]
-RP   1-1859
-RA   Hughes M.A.;
-RT   ;
-RL   Submitted (19-NOV-1990) to the INSDC.
-RL   Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle
-RL   Upon Tyne, NE2 4HH, UK
-XX
-DR   EuropePMC; PMC99098; 11752244.
-XX
-FH   Key             Location/Qualifiers
-FH
-FT   source          1..1859
-FT                   /organism="Trifolium repens"
-FT                   /mol_type="mRNA"
-FT                   /clone_lib="lambda gt10"
-FT                   /clone="TRE361"
-FT                   /tissue_type="leaves"
-FT                   /db_xref="taxon:3899"
-FT   mRNA            1..1859
-FT                   /experiment="experimental evidence, no additional details
-FT                   recorded"
-FT   CDS             14..1495
-FT                   /product="beta-glucosidase"
-FT                   /EC_number="3.2.1.21"
-FT                   /note="non-cyanogenic"
-FT                   /db_xref="GOA:P26204"
-FT                   /db_xref="InterPro:IPR001360"
-FT                   /db_xref="InterPro:IPR013781"
-FT                   /db_xref="InterPro:IPR017853"
-FT                   /db_xref="InterPro:IPR018120"
-FT                   /db_xref="UniProtKB/Swiss-Prot:P26204"
-FT                   /protein_id="CAA40058.1"
-FT                   /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI
-FT                   FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK
-FT                   DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ
-FT                   VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR
-FT                   CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD
-FT                   DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF
-FT                   IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ
-FT                   EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA
-FT                   IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD"
-XX
-SQ   Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
-     aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt        60
-     cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag       120
-     tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga       180
-     aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata       240
-     tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta       300
-     caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc       360
-     ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa       420
-     atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct       480
-     ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg       540
-     tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt       600
-     gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg       660
-     aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac       720
-     aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta       780
-     taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg       840
-     gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga       900
-     cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg       960
-     gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg      1020
-     ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc      1080
-     acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa      1140
-     acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat      1200
-     gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct      1260
-     gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga      1320
-     agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg      1380
-     ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg      1440
-     taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga      1500
-     tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa      1560
-     ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt      1620
-     tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg      1680
-     aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc      1740
-     agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac      1800
-     tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa       1859
-//
+::
+
+    ID   X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP.
+    XX
+    AC   X56734; S46826;
+    XX
+    DT   12-SEP-1991 (Rel. 29, Created)
+    DT   25-NOV-2005 (Rel. 85, Last updated, Version 11)
+    XX
+    DE   Trifolium repens mRNA for non-cyanogenic beta-glucosidase
+    XX
+    KW   beta-glucosidase.
+    XX
+    OS   Trifolium repens (white clover)
+    OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
+    OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
+    OC   fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium.
+    XX
+    RN   [5]
+    RP   1-1859
+    RX   DOI; 10.1007/BF00039495.
+    RX   PUBMED; 1907511.
+    RA   Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
+    RT   "Nucleotide and derived amino acid sequence of the cyanogenic
+    RT   beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
+    RL   Plant Mol. Biol. 17(2):209-219(1991).
+    XX
+    RN   [6]
+    RP   1-1859
+    RA   Hughes M.A.;
+    RT   ;
+    RL   Submitted (19-NOV-1990) to the INSDC.
+    RL   Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle
+    RL   Upon Tyne, NE2 4HH, UK
+    XX
+    DR   EuropePMC; PMC99098; 11752244.
+    XX
+    FH   Key             Location/Qualifiers
+    FH
+    FT   source          1..1859
+    FT                   /organism="Trifolium repens"
+    FT                   /mol_type="mRNA"
+    FT                   /clone_lib="lambda gt10"
+    FT                   /clone="TRE361"
+    FT                   /tissue_type="leaves"
+    FT                   /db_xref="taxon:3899"
+    FT   mRNA            1..1859
+    FT                   /experiment="experimental evidence, no additional details
+    FT                   recorded"
+    FT   CDS             14..1495
+    FT                   /product="beta-glucosidase"
+    FT                   /EC_number="3.2.1.21"
+    FT                   /note="non-cyanogenic"
+    FT                   /db_xref="GOA:P26204"
+    FT                   /db_xref="InterPro:IPR001360"
+    FT                   /db_xref="InterPro:IPR013781"
+    FT                   /db_xref="InterPro:IPR017853"
+    FT                   /db_xref="InterPro:IPR018120"
+    FT                   /db_xref="UniProtKB/Swiss-Prot:P26204"
+    FT                   /protein_id="CAA40058.1"
+    FT                   /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI
+    FT                   FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK
+    FT                   DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ
+    FT                   VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR
+    FT                   CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD
+    FT                   DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF
+    FT                   IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ
+    FT                   EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA
+    FT                   IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD"
+    XX
+    SQ   Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
+         aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt        60
+         cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag       120
+         tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga       180
+         aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata       240
+         tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta       300
+         caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc       360
+         ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa       420
+         atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct       480
+         ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg       540
+         tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt       600
+         gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg       660
+         aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac       720
+         aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta       780
+         taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg       840
+         gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga       900
+         cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg       960
+         gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg      1020
+         ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc      1080
+         acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa      1140
+         acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat      1200
+         gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct      1260
+         gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga      1320
+         agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg      1380
+         ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg      1440
+         taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga      1500
+         tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa      1560
+         ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt      1620
+         tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg      1680
+         aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc      1740
+         agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac      1800
+         tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa       1859
+    //