(* TODO *)

Ocamllex template

This is an example of using ocamllex for parsing structured text using ocamllex entirely. The language (Genbank format) is not yacc-friendly because tokens can't be extracted in a single pass independently from grammar rules.

Input data:

LOCUS       AB000684                 275 bp    DNA     linear   ENV 29-JUL-2005
DEFINITION  Uncultured bacterium gene for 16S rRNA, partial sequence, clone: 2

            of cluster I.

ACCESSION   AB000684

VERSION     AB000684.1  GI:1817504

KEYWORDS    ENV.

SOURCE      uncultured bacterium

  ORGANISM  uncultured bacterium

            Bacteria; environmental samples.

REFERENCE   1

  AUTHORS   Inagaki,F., Hayashi,S., Doi,K., Motomura,Y., Izawa,E. and Ogata,S.

  TITLE     Microbial participation in the formation of siliceous deposits from

            geothermal water and analysis of the extremely thermophilic

            bacterial community

  JOURNAL   FEMS Microbiol. Ecol. 24, 41-48 (1997)

REFERENCE   2  (bases 1 to 275)

  AUTHORS   Inagaki,F., Hayashi,S., Doi,K., Motomura,Y., Izawa,E. and Ogata,S.

  TITLE     Direct Submission

  JOURNAL   Submitted (24-JAN-1997) Fumio Inagaki, Faculty of Agriculture,

            Kyushu University, Microbial Genetic Division, Institute of Genetic

            Resourses; Higashi-ku Hakozaki 6-10-1, Fukuoka-shi, Fukuoka 812-81,

            Japan (E-mail:inagaki@agr.kyushu-u.ac.jp, Tel:+81-92-642-3059,

            Fax:+81-92-642-3059)

FEATURES             Location/Qualifiers

     source          1..275

                     /organism="uncultured bacterium"

                     /mol_type="genomic DNA"

                     /db_xref="taxon:77133"

                     /clone="2 of cluster I"

                     /environmental_sample

     rRNA            <1..>275

                     /product="16S ribosomal RNA"

ORIGIN      

        1 ctgcccttag ttgccactct tcggagggca ctctaagggg accgccggcg ataagccgag

       61 gaaggtgggg atgacgtcag gtcagtatgc cctttatgcc cggggctaca caggcgctac

      121 agtggccagg acaatgggaa gcgacccagt aatggggagc aaatccctaa acctggtcat

      181 ggtgcagatt gagggctgaa actcgcccct catgaagccg gaatcggtag taatggcgga

      241 tcagctaagc cgccgtgaat acgttctcgg gcctt

//

Template for the corresponding ocamllex parser (file genbank.mll):

{  type record = {
    mutable locus : ...;

    mutable definition : string option;

    mutable accession : ...;

    ...

  }



  let new_record () = {

    locus = None;

    definition = None;

    accession = None;

    ...

  }



  let newline lexbuf =

    ...

    (* would set the correct line count

       for useful error messages *)

}



rule top record = parse

  "LOCUS       " ...

   { ... }

| "DEFINITION  " ([^'\r' '\n']+ as text) '\r'? '\n'

   {

     newline lexbuf;

     let def_text = continue_definition [text] lexbuf in

     if record.definition <> None then

       ... (* error: multiple DEFINITION fields *);

     record.definition <- Some def_text

   }

| "ACCESSION   " ...

   { ... }

...

| "//" '\r'? '\n'

   {

     newline lexbuf;

     Some record

   }

| eof

   {

     ... ; (* check that the current record is empty *)

     None

   }

| ""

   { (* report error *) }





and continue_definition accu = parse

  "            " ([^'\r' '\n']+ as text) '\r'? '\n'

   {

     newline lexbuf;

     continue_definition (text :: accu) lexbuf

   }

| ""

   { String.concat " " (List.rev accu) }





{

  let rec scan process_record lexbuf =

    match top (new_record ()) lexbuf with

        None -> ()

      | Some x ->

          process_record x;

          scan process_record lexbuf

}