[Biojava-l] BiojavaX EmblFormat

Thu Mar 9 01:02:09 UTC 2006

The biojavax parser uses regular expressions to parse these lines. I will 
need to check what needs changing in these regex's to allow parsing of 
these files.

Thanks for your testing!

- Mark

"Jolyon Holdstock" <jolyon.holdstock at ogt.co.uk>
Sent by: biojava-l-bounces at portal.open-bio.org
03/08/2006 06:47 PM

        To:     <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] BiojavaX EmblFormat

Hi,

I am using the new format parsers in BioJavaX. GenbankFormat is great,
but I am having some trouble with the EMBLFormat class. I have
downloaded a sequence file (ID:U00096) from the EBI in EMBL format but I
don't believe it is parsing properly.

My code is as follows:

String fileName = "path to file";

try {

  RichSequenceIterator rsi = RichSequence.IOTools.readEMBLDNA(new
BufferedReader(new FileReader(fileName)), null);

  while (rsi.hasNext()) {

    RichSequence seq = rsi.nextRichSequence();

    System.out.println(seq.getURN());

    System.out.println(seq.length());

    System.out.println(seq.getAccession());

  }

}

catch (IOException IOE) {

  System.out.println("BioJava IOException " + IOE);

}

catch (BioException BIOE) {

  System.out.println("BioJavaX BioException " + BIOE);

  BIOE.printStackTrace(); 

}

The BioJava parser will read it.

seq = SeqIOTools.readEmbl(new BufferedReader(new
FileReader(fileName))).nextSequence(); //works

I checked the web CVS and the EMBLFormat class is 3 months old so I am
using the most recent version.

I have pasted a snippet of the sequence file that retains the problems
below.

The errors are:

The ID line isn't parsed because of 'genomic' being there - deleting it
removes the problem

org.biojava.bio.BioException: Could not read sequence

Caused by: org.biojava.bio.seq.io.ParseException: 

    Bad ID line found: U00096     standard; circular genomic DNA; PRO;
4639675 BP.

ID   U00096     standard; circular genomic DNA; PRO; 4639675 BP. //fails

ID   U00096     standard; circular DNA; PRO; 4639675 BP. //works

There is a problem with the RX tag which fails with output:

org.biojava.bio.BioException: Could not read sequence

Caused by: java.lang.ArrayIndexOutOfBoundsException: 1

      at
org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:352)

Replacing 
RX   DOI; 10.1126/science.277.5331.1453.

with removes the error 

XX   RX   DOI; 10.1126/science.277.5331.1453.

There is an error with parsing the authors

org.biojava.bio.BioException: Could not read sequence

Caused by: java.lang.IllegalArgumentException: Authors string cannot be
null

      at
org.biojavax.DocRefAuthor$Tools.parseAuthorString(DocRefAuthor.java:75)

      at
org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:395)

      at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamRead
er.java:100)

I am looking at the code trying to see where the problems are but
suspect that it may be beyond me.

So if anybody has some experience of this I would welcome their input.

Thanks,

Jolyon

This is a snippet of the code that reproduces the errors in my hands.

ID   U00096     standard; circular genomic DNA; PRO; 4639675 BP.

XX

AC   U00096; AE000111-AE000510;

XX

SV   U00096.2

XX

DT   23-FEB-2006 (Rel. 86, Created)

DT   06-MAR-2006 (Rel. 87, Last updated, Version 3)

XX

DE   Escherichia coli K-12 MG1655, complete genome.

XX

KW   .

XX

OS   Escherichia coli K12

OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;

OC   Enterobacteriaceae; Escherichia.

XX

RN   [1]

RP   1-4639675

RX   DOI; 10.1126/science.277.5331.1453.

RX   PUBMED; 9278503.

RA   Blattner F.R., Plunkett G., Bloch C.A., Perna N.T., Burland V.,
Riley M.,

RA   Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J.,

RA   Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao
Y.;

RT   "The complete genome sequence of Escherichia coli K-12";

RL   Science 277(5331):1453-1474(1997).

XX

RN   [2]

RP   1-4639675

RX   DOI; 10.1093/nar/gkj150.

RX   PUBMED; 16397293.

RA   Riley M., Abe T., Arnaud M.B., Berlyn M.K., Blattner F.R.,
Chaudhuri R.R.,

RA   Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna
N.T.,

RA   Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R.,

RA   Wishart D., Wanner B.L.;

RT   "Escherichia coli K-12: a cooperatively developed annotation

RT   snapshot--2005";

RL   (er) Nucleic Acids Res. 34 (1), 1-9 (2006)

XX

RN   [3]

RC   Woods Hole, Mass., on 14-18 November 2003 (sequence corrections)

RP   1-4639675

RA   Arnaud M., Berlyn M.K.B., Blattner F.R., Galperin M.Y., Glasner
J.D.,

RA   Horiuchi T., Kosuge T., Mori H., Perna N.T., Plunkett G. III, Riley
M.,

RA   Rudd K.E., Serres M.H., Thomas G.H., Wanner B.L.;

RT   "Workshop on Annotation of Escherichia coli K-12";

RL   Unpublished.

XX

RN   [4]

RC   ASAP download 10 June 2004 (annotation updates)

RP   1-4639675

RA   Glasner J.D., Perna N.T., Plunkett G. III, Anderson B.D., Bockhorst
J.,

RA   Hu J.C., Riley M., Rudd K.E., Serres M.H.;

RT   "ASAP: Escherichia coli K-12 strain MG1655 version m56";

RL   Unpublished.

XX

RN   [5]

RC   GenBank accessions AG613214 to AG613378 (sequence corrections)

RP   1-4639675

RA   Hayashi K., Morooka N., Mori H., Horiuchi T.;

RT   "A more accurate sequence comparison between genomes of Escherichia
coli

RT   K12 W3110 and MG1655 strains";

RL   Unpublished.

XX

RN   [6]

RC   GenBank accession AY605712 (sequence corrections)

RP   1-4639675

RA   Perna N.T.;

RT   "Escherichia coli K-12 MG1655 yqiK-rfaE intergenic region, genomic
sequence

RT   correction";

RL   Unpublished.

XX

RN   [7]

RP   1-4639675

RA   Rudd K.E.;

RT   "A manual approach to accurate translation start site annotation:
an E.

RT   coli K-12 case study";

RL   Unpublished.

XX

RN   [8]

RP   1-4639675

RA   Blattner F.R., Plunkett G. III.;

RT   ;

RL   Submitted (16-JAN-1997) to the EMBL/GenBank/DDBJ databases.