:) I got another one for you:
=========================
org.biojava.bio.BioException: Could not read sequence
at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
at exonhit.parsers.GenBankParser.main(GenBankParser.java:348)
Caused by: java.lang.StringIndexOutOfBoundsException: String index out
of range: -3
at java.lang.String.substring(String.java:1768)
at java.lang.String.substring(String.java:1735)
at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:672)
at
org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:281)
at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
... 1 more
Java Result: -1
=========================
File used to produce the above:
~~~~~~~~~~~~~~~~~~~~~~~~~
ID DQ472184 standard; DNA; INV; 546 BP.
XX
AC DQ472184;
XX
SV DQ472184.1
DT 15-MAY-2006
XX
DE Trypanosoma cruzi strain CL Brener actin-related protein 3 (ARC21) gene,
DE complete cds.
XX
KW .
XX
OS Trypanosoma cruzi strain CL Brener
OC Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma;
OC Schizotrypanum.
XX
RN [1]
RP 1-546
RA De Melo L.D.B.;
RT "Actin of Trypanosoma cruzi: ubiquitous actin-binding proteins";
RL Unpublished.
XX
RN [2]
RP 1-546
RA De Melo L.D.B.;
RT ;
RL Submitted (03-APR-2006) to the EMBL/GenBank/DDBJ databases.
RL Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio
RL de Janeiro, Cidade Universitaria, CCS, Bl.G, Sl.G157, Rio de Janeiro, RJ
RL 21949-900, Brazil
XX
FH Key Location/Qualifiers
FH
FT source 1..546
FT /organism="Trypanosoma cruzi strain CL Brener"
FT /mol_type="genomic DNA"
FT /strain="CL Brener"
FT /db_xref="taxon:353153"
FT gene <1..>546
FT /gene="ARC21"
FT /note="TcARC21"
FT mRNA <1..>546
FT /gene="ARC21"
FT /product="actin-related protein 3"
FT CDS 1..546
FT /gene="ARC21"
FT /note="actin-binding protein; ARPC3 21 kDa; putative
FT member of Arp2/3 complex"
FT /codon_start=1
FT /product="actin-related protein 3"
FT /protein_id="ABF13401.1"
FT /db_xref="GI:93360014"
FT /translation="MHSRWNGYEESSLLGCGVYPLRRTSRLTPPGPAPRMDEMIEEG
FT EEEPQDIVDEAFYFFKPHMFFRNFPIKGAGDRVILYLTMYLHECLKKIVQLKREEAH
FT SVLLNYATMPFASPGEKDFPFNAFFPAGNEEEQEKWREYAKQLRLEANARLIEKVFL
FT FPEKDGTGNKFWMAFAKRPFLASS"
atgcacagca ggtggaatgg gtatgaagaa agtagtcttt tgggctgcgg tgtttatccg 60
cttcgccgca cgtcacggct cactccaccc ggccctgcac cgcggatgga tgaaatgatt 120
gaggagggcg aagaggagcc acaagacatt gttgacgagg cattttactt ttttaagccc 180
cacatgtttt ttcgtaattt tcccattaag ggtgctggtg atcgtgtcat tctgtacttg 240
acgatgtacc ttcatgagtg tttgaagaaa attgtccagt tgaagcgtga agaggcccat 300
tctgtgcttc ttaactacgc tacgatgccg tttgcatcac caggggaaaa ggactttccg 360
tttaacgcgt ttttccctgc tgggaatgag gaggaacaag aaaaatggcg agagtatgca 420
aaacagcttc gattggaggc caacgcacgt ctcattgaga aggtttttct ttttccagag 480
aaggacggca ccggaaacaa gttctggatg gcgtttgcga agaggccttt cttggcttct 540
agttag 546
//
ID DQ472185 standard; DNA; INV; 543 BP.
XX
AC DQ472185;
XX
SV DQ472185.1
DT 15-MAY-2006
XX
DE Trypanosoma cruzi strain CL Brener actin-related protein 4 (ARC20) gene,
DE complete cds.
XX
KW .
XX
OS Trypanosoma cruzi strain CL Brener
OC Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma;
OC Schizotrypanum.
XX
RN [1]
RP 1-543
RA De Melo L.D.B.;
RT "Actin of Trypanosoma cruzi: ubiquitous actin-binding proteins";
RL Unpublished.
XX
RN [2]
RP 1-543
RA De Melo L.D.B.;
RT ;
RL Submitted (03-APR-2006) to the EMBL/GenBank/DDBJ databases.
RL Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio
RL de Janeiro, Cidade Universitaria, CCS, Bl.G, Sl.G157, Rio de Janeiro, RJ
RL 21949-900, Brazil
XX
FH Key Location/Qualifiers
FH
FT source 1..543
FT /organism="Trypanosoma cruzi strain CL Brener"
FT /mol_type="genomic DNA"
FT /strain="CL Brener"
FT /db_xref="taxon:353153"
FT gene <1..>543
FT /gene="ARC20"
FT /note="TcARC20"
FT mRNA <1..>543
FT /gene="ARC20"
FT /product="actin-related protein 4"
FT CDS 1..543
FT /gene="ARC20"
FT /note="actin-binding protein; ARPC4 20 kDa; putative
FT member of Arp2/3 complex"
FT /codon_start=1
FT /product="actin-related protein 4"
FT /protein_id="ABF13402.1"
FT /db_xref="GI:93360016"
FT /translation="MATAYLPYYDCIKCTLHAALCIGNYPSCTVERHNKPEVEVADH
FT LENNGEIKVQDFLLNPIRIVRSEQESCLIEPSINSTRISVSFLKSDAIAEIIARKYV
FT GFLAQRAKQFHILRKKPIPGYDISFLISHEEVETMHRNRIIQFIITFLMDIDADIAA
FT MKLNVNQRARRAAMEFFLALNFT"
atggcaaccg cctatttgcc ttactacgac tgcatcaagt gcacgttgca cgcggctttg 60
tgcatcggga attatccttc atgtaccgtg gagcgtcata ataaaccaga agttgaggtt 120
gcagaccatc tggagaataa tggtgaaata aaagtacaag atttccttct taaccccata 180
cgcattgtgc gttcagaaca ggaaagttgt cttattgaac ctagtataaa cagcacacgc 240
atatctgtat cgtttctcaa gagcgacgct attgcagaga ttattgcccg aaagtacgtt 300
ggatttttag ctcagcgagc caaacagttt cacatcttga gaaaaaagcc tattccggga 360
tatgatataa gttttttgat ttctcacgag gaagtagaaa caatgcatag gaataggatt 420
attcaattta taattacttt cttgatggat attgatgctg acattgctgc aatgaagttg 480
aatgtgaatc aacgtgcacg tcgagcagcg atggaattct ttcttgcatt gaatttcaca 540
tga 543
//
~~~~~~~~~~~~~~~~~~~~~~~~~
On 6/5/06, Richard Holland <[EMAIL PROTECTED]> wrote:
> Doh!
>
> I am in desparate need of coffee methinks... that's the second error in
> EMBLFormat directly related to me being stupid when I cut-and-pasted the
> stuff for the new 87+ ID line format...
>
> Should be fixed now in CVS (as of about 30 seconds ago).
>
> cheers,
> Richard
>
> On Mon, 2006-06-05 at 11:05 -0400, Seth Johnson wrote:
> > Hi Richard,
> >
> > I go another exception on EMBL format:
> > =============================
> > org.biojava.bio.BioException: Could not read sequence
> > at
> > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
> > at exonhit.parsers.GenBankParser.main(GenBankParser.java:347)
> > Caused by: java.lang.IllegalStateException: No match found
> > at java.util.regex.Matcher.group(Matcher.java:461)
> > at
> > org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:311)
> > at
> > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
> > ... 1 more
> > Java Result: -1
> > =============================
> > I used the same file from test directory:(AY069118.em)
> >
> >
> > Seth
> >
> > On 6/5/06, Richard Holland <[EMAIL PROTECTED]> wrote:
> > > This one should be fixed in CVS now. Typo on my behalf - I put in code
> > > to make it work with both 87+ and pre-87 version of EMBL, then got the
> > > regexes the wrong way round!!
> > >
> > ...
> > >
> > > cheers,
> > > Richard
> > >
> > >
> > > On Fri, 2006-06-02 at 13:04 -0400, Seth Johnson wrote:
> > > > Hi Richard,
> > > >
> > > > I made sure I have the latest source code from CVS compiled
> > > > (EMBLFormat.java & GenbankFormat.java are from 05/24/06). I'm happy
> > > > to report that GenBank issue is solved!!!!
> > > > As far as EMBL parsing, I apologize for not providing the stack dump
> > > > for ISSUE #1. Here's the dump of the exception:
> > > > --------------------------------------------------------
> > > > org.biojava.bio.BioException: Could not read sequence
> > > > at
> > > > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
> > > > at exonhit.parsers.GenBankParser.main(GenBankParser.java:359)
> > > > Caused by: java.lang.NumberFormatException: null
> > > > at java.lang.Integer.parseInt(Integer.java:415)
> > > > at java.lang.Integer.parseInt(Integer.java:497)
> > > > at
> > > > org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:299)
> > > > at
> > > > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
> > > > ... 1 more
> > > > Java Result: -1
> > > > -------------------------------------------------------
> > > > Here, again, is the code that I'm using to to parse:
> > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > > > BufferedReader gbBR = null;
> > > > try {
> > > > gbBR = new BufferedReader(new
> > > > FileReader("C:\\Download\\ASN2BSML\\seth_06_02.emb"));
> > > > } catch (FileNotFoundException fnfe) {
> > > > fnfe.printStackTrace();
> > > > System.exit(-1);
> > > > }
> > > > Namespace gbNspace = (Namespace)
> > > > RichObjectFactory.getObject(SimpleNamespace.class, new
> > > > Object[]{"gbSpace"} );
> > > > RichSequenceIterator gbSeqs =
> > > > RichSequence.IOTools.readEMBLDNA(gbBR,gbNspace);
> > > > while (gbSeqs.hasNext()) {
> > > > try {
> > > > RichSequence rs = gbSeqs.nextRichSequence();
> > > > NCBITaxon myTaxon = rs.getTaxon();
> > > > }catch (BioException be){
> > > > be.printStackTrace();
> > > > System.exit(-1);
> > > > }
> > > > }
> > > > ~~~~~~~~~~~~~~~~~~~~~~~~~
> > > > And here's the EMBL file that I'm trying to parse:
> > > > +++++++++++++++++++++++++
> > > > ID DQ472184 standard; DNA; INV; 546 BP.
> > > > XX
> > > > AC DQ472184;
> > > > XX
> > > > SV DQ472184.1
> > > > DT 15-MAY-2006
> > > > XX
> > > > DE Trypanosoma cruzi strain CL Brener actin-related protein 3 (ARC21)
> > > > gene,
> > > > DE complete cds.
> > > > XX
> > > > KW .
> > > > XX
> > > > OS Trypanosoma cruzi strain CL Brener
> > > > OC Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
> > > > Trypanosoma;
> > > > OC Schizotrypanum.
> > > > XX
> > > > RN [1]
> > > > RP 1-546
> > > > RA De Melo L.D.B.;
> > > > RT "Actin of Trypanosoma cruzi: ubiquitous actin-binding proteins";
> > > > RL Unpublished.
> > > > XX
> > > > RN [2]
> > > > RP 1-546
> > > > RA De Melo L.D.B.;
> > > > RT ;
> > > > RL Submitted (03-APR-2006) to the EMBL/GenBank/DDBJ databases.
> > > > RL Instituto de Biofisica Carlos Chagas Filho, Universidade Federal
> > > > do Rio
> > > > RL de Janeiro, Cidade Universitaria, CCS, Bl.G, Sl.G157, Rio de
> > > > Janeiro, RJ
> > > > RL 21949-900, Brazil
> > > > XX
> > > > FH Key Location/Qualifiers
> > > > FH
> > > > FT source 1..546
> > > > FT /organism="Trypanosoma cruzi strain CL Brener"
> > > > FT /mol_type="genomic DNA"
> > > > FT /strain="CL Brener"
> > > > FT /db_xref="taxon:353153"
> > > > FT gene <1..>546
> > > > FT /gene="ARC21"
> > > > FT /note="TcARC21"
> > > > FT mRNA <1..>546
> > > > FT /gene="ARC21"
> > > > FT /product="actin-related protein 3"
> > > > FT CDS 1..546
> > > > FT /gene="ARC21"
> > > > FT /note="actin-binding protein; ARPC3 21 kDa;
> > > > putative
> > > > FT member of Arp2/3 complex"
> > > > FT /codon_start=1
> > > > FT /product="actin-related protein 3"
> > > > FT /protein_id="ABF13401.1"
> > > > FT /db_xref="GI:93360014"
> > > > FT
> > > > /translation="MHSRWNGYEESSLLGCGVYPLRRTSRLTPPGPAPRMDEMIEEG
> > > > FT
> > > > EEEPQDIVDEAFYFFKPHMFFRNFPIKGAGDRVILYLTMYLHECLKKIVQLKREEAH
> > > > FT
> > > > SVLLNYATMPFASPGEKDFPFNAFFPAGNEEEQEKWREYAKQLRLEANARLIEKVFL
> > > > FT FPEKDGTGNKFWMAFAKRPFLASS"
> > > > atgcacagca ggtggaatgg gtatgaagaa agtagtcttt tgggctgcgg tgtttatccg
> > > > 60
> > > > cttcgccgca cgtcacggct cactccaccc ggccctgcac cgcggatgga tgaaatgatt
> > > > 120
> > > > gaggagggcg aagaggagcc acaagacatt gttgacgagg cattttactt ttttaagccc
> > > > 180
> > > > cacatgtttt ttcgtaattt tcccattaag ggtgctggtg atcgtgtcat tctgtacttg
> > > > 240
> > > > acgatgtacc ttcatgagtg tttgaagaaa attgtccagt tgaagcgtga agaggcccat
> > > > 300
> > > > tctgtgcttc ttaactacgc tacgatgccg tttgcatcac caggggaaaa ggactttccg
> > > > 360
> > > > tttaacgcgt ttttccctgc tgggaatgag gaggaacaag aaaaatggcg agagtatgca
> > > > 420
> > > > aaacagcttc gattggaggc caacgcacgt ctcattgaga aggtttttct ttttccagag
> > > > 480
> > > > aaggacggca ccggaaacaa gttctggatg gcgtttgcga agaggccttt cttggcttct
> > > > 540
> > > > agttag
> > > > 546
> > > > //
> > > > ID DQ472185 standard; DNA; INV; 543 BP.
> > > > XX
> > > > AC DQ472185;
> > > > XX
> > > > SV DQ472185.1
> > > > DT 15-MAY-2006
> > > > XX
> > > > DE Trypanosoma cruzi strain CL Brener actin-related protein 4 (ARC20)
> > > > gene,
> > > > DE complete cds.
> > > > XX
> > > > KW .
> > > > XX
> > > > OS Trypanosoma cruzi strain CL Brener
> > > > OC Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
> > > > Trypanosoma;
> > > > OC Schizotrypanum.
> > > > XX
> > > > RN [1]
> > > > RP 1-543
> > > > RA De Melo L.D.B.;
> > > > RT "Actin of Trypanosoma cruzi: ubiquitous actin-binding proteins";
> > > > RL Unpublished.
> > > > XX
> > > > RN [2]
> > > > RP 1-543
> > > > RA De Melo L.D.B.;
> > > > RT ;
> > > > RL Submitted (03-APR-2006) to the EMBL/GenBank/DDBJ databases.
> > > > RL Instituto de Biofisica Carlos Chagas Filho, Universidade Federal
> > > > do Rio
> > > > RL de Janeiro, Cidade Universitaria, CCS, Bl.G, Sl.G157, Rio de
> > > > Janeiro, RJ
> > > > RL 21949-900, Brazil
> > > > XX
> > > > FH Key Location/Qualifiers
> > > > FH
> > > > FT source 1..543
> > > > FT /organism="Trypanosoma cruzi strain CL Brener"
> > > > FT /mol_type="genomic DNA"
> > > > FT /strain="CL Brener"
> > > > FT /db_xref="taxon:353153"
> > > > FT gene <1..>543
> > > > FT /gene="ARC20"
> > > > FT /note="TcARC20"
> > > > FT mRNA <1..>543
> > > > FT /gene="ARC20"
> > > > FT /product="actin-related protein 4"
> > > > FT CDS 1..543
> > > > FT /gene="ARC20"
> > > > FT /note="actin-binding protein; ARPC4 20 kDa;
> > > > putative
> > > > FT member of Arp2/3 complex"
> > > > FT /codon_start=1
> > > > FT /product="actin-related protein 4"
> > > > FT /protein_id="ABF13402.1"
> > > > FT /db_xref="GI:93360016"
> > > > FT
> > > > /translation="MATAYLPYYDCIKCTLHAALCIGNYPSCTVERHNKPEVEVADH
> > > > FT
> > > > LENNGEIKVQDFLLNPIRIVRSEQESCLIEPSINSTRISVSFLKSDAIAEIIARKYV
> > > > FT
> > > > GFLAQRAKQFHILRKKPIPGYDISFLISHEEVETMHRNRIIQFIITFLMDIDADIAA
> > > > FT MKLNVNQRARRAAMEFFLALNFT"
> > > > atggcaaccg cctatttgcc ttactacgac tgcatcaagt gcacgttgca cgcggctttg
> > > > 60
> > > > tgcatcggga attatccttc atgtaccgtg gagcgtcata ataaaccaga agttgaggtt
> > > > 120
> > > > gcagaccatc tggagaataa tggtgaaata aaagtacaag atttccttct taaccccata
> > > > 180
> > > > cgcattgtgc gttcagaaca ggaaagttgt cttattgaac ctagtataaa cagcacacgc
> > > > 240
> > > > atatctgtat cgtttctcaa gagcgacgct attgcagaga ttattgcccg aaagtacgtt
> > > > 300
> > > > ggatttttag ctcagcgagc caaacagttt cacatcttga gaaaaaagcc tattccggga
> > > > 360
> > > > tatgatataa gttttttgat ttctcacgag gaagtagaaa caatgcatag gaataggatt
> > > > 420
> > > > attcaattta taattacttt cttgatggat attgatgctg acattgctgc aatgaagttg
> > > > 480
> > > > aatgtgaatc aacgtgcacg tcgagcagcg atggaattct ttcttgcatt gaatttcaca
> > > > 540
> > > > tga
> > > > 543
> > > > //
> > > > +++++++++++++++++++++++++++++++++
> > > >
> > > > It looks to me like there's some kind of problem with parsing the
> > > > sequence version number. I even tried the sequence from test directory
> > > > (AY069118.em) with same outcome.
> > > >
> > > > Regards,
> > > >
> > > > Seth
> > > >
> > > > On 6/2/06, Richard Holland <[EMAIL PROTECTED]> wrote:
> > > > > Hi Seth.
> > > > >
> > > > > Your second point, about the authors string not being read correctly
> > > > > in
> > > > > Genbank format, has been fixed (or should have been if I got the code
> > > > > right!). Could you check the latest version of biojava-live out of CVS
> > > > > and give it another go? Basically the parser did not recognise the
> > > > > CONSRTM tag, as it is not mentioned in the sample record provided by
> > > > > NCBI, which is what I based the parser on.
> > > > >
> > > > > I've set it up now so that it reads the CONSRTM tag, but the value is
> > > > > merged with the authors tag with (consortium) appended. There will
> > > > > still
> > > > > be problems if the consortium value has commas in it - not sure how to
> > > > > fix this yet.
> > > > >
> > > > > Your first point is harder to solve because you did not provide a
> > > > > complete stack trace for the exceptions you are getting. The complete
> > > > > stack trace would enable me to identify exactly where things are going
> > > > > wrong and give me a better chance of fixing them. Could you send the
> > > > > stack trace, and I'll see what I can do.
> > > > >
> > > > > cheers,
> > > > > Richard
> > > > >
> > > > >
> > > > > On Thu, 2006-06-01 at 18:03 -0400, Seth Johnson wrote:
> > > > > > Hi All,
> > > > > >
> > > > > > I'm a newbie to the whole BioJava(X) API and was hoping to get some
> > > > > > clarification on several issues that I'm having.
> > > > > > I am developing a parser that would take as input "NCBI Incremental
> > > > > > ASN.1 Sequence Updates to Genbank" files (
> > > > > > ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc ) , gunzip them, and use
> > > > > > the
> > > > > > ASN2GB converter (
> > > > > > ftp://ftp.ncbi.nih.gov/asn1-converters/by_program/asn2gb ) to
> > > > > > convert
> > > > > > resulting sequences to a format parsable by BioJava(X) (
> > > > > > http://www.penguin-soft.com/penguin/man/1/asn2gb.html ). This is
> > > > > > where
> > > > > > my problems start.
> > > > > >
> > > > > > ISSUE 1:
> > > > > > I've tried to parse all of the formats that ASN2GB outputs ( GenBank
> > > > > > (default) , EMBL, nucleotide GBSet (XML), nucleotide INSDSet (XML),
> > > > > > tiny seq (XML) ) using either BioJava or BioJavaX API. Only GenBank
> > > > > > format is recognized by the
> > > > > > "RichSequence.IOTools.readGenbankDNA(inBuf,gbNspace)" function with
> > > > > > some exceptions that I'll describe in issue #2. This is the code
> > > > > > that
> > > > > > I'm using to parse, for example, the EMBL output:
> > > > > >
> > > > > > BufferedReader inBuf = new BufferedReader(new
> > > > > > FileReader("embl_output.emb"));
> > > > > > Namespace gbNspace = (Namespace)
> > > > > > RichObjectFactory.getObject(SimpleNamespace.class, new
> > > > > > Object[]{"gbSpace"} );
> > > > > > RichSequenceIterator gbSeqs =
> > > > > > RichSequence.IOTools.readEMBLDNA(inBuf,gbNspace);
> > > > > > while (gbSeqs.hasNext()) {
> > > > > > try {
> > > > > > RichSequence rs = gbSeqs.nextRichSequence();
> > > > > > // Further processing or RichSequence object from here
> > > > > >
> > > > > > } catch (BioException be){
> > > > > > be.printStackTrace();
> > > > > > }
> > > > > > }
> > > > > >
> > > > > > The multi-sequence EMBL file looks like this:
> > > > > > ---------------------------------------------------------------------------------
> > > > > > ID DQ472184 standard; DNA; INV; 546 BP.
> > > > > > XX
> > > > > > AC DQ472184;
> > > > > > XX
> > > > > > SV DQ472184.1
> > > > > > DT 15-MAY-2006
> > > > > > XX
> > > > > > DE Trypanosoma cruzi strain CL Brener actin-related protein 3
> > > > > > (ARC21) gene,
> > > > > > DE complete cds.
> > > > > > XX
> > > > > > KW .
> > > > > > XX
> > > > > > OS Trypanosoma cruzi strain CL Brener
> > > > > > OC Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
> > > > > > Trypanosoma;
> > > > > > OC Schizotrypanum.
> > > > > > XX
> > > > > > RN [1]
> > > > > > RP 1-546
> > > > > > RA De Melo L.D.B.;
> > > > > > RT "Actin of Trypanosoma cruzi: ubiquitous actin-binding
> > > > > > proteins";
> > > > > > RL Unpublished.
> > > > > > XX
> > > > > > RN [2]
> > > > > > RP 1-546
> > > > > > RA De Melo L.D.B.;
> > > > > > RT ;
> > > > > > RL Submitted (03-APR-2006) to the EMBL/GenBank/DDBJ databases.
> > > > > > RL Instituto de Biofisica Carlos Chagas Filho, Universidade
> > > > > > Federal do Rio
> > > > > > RL de Janeiro, Cidade Universitaria, CCS, Bl.G, Sl.G157, Rio de
> > > > > > Janeiro, RJ
> > > > > > RL 21949-900, Brazil
> > > > > > XX
> > > > > > FH Key Location/Qualifiers
> > > > > > FH
> > > > > > FT source 1..546
> > > > > > FT /organism="Trypanosoma cruzi strain CL Brener"
> > > > > > FT /mol_type="genomic DNA"
> > > > > > FT /strain="CL Brener"
> > > > > > FT /db_xref="taxon:353153"
> > > > > > FT gene <1..>546
> > > > > > FT /gene="ARC21"
> > > > > > FT /note="TcARC21"
> > > > > > FT mRNA <1..>546
> > > > > > FT /gene="ARC21"
> > > > > > FT /product="actin-related protein 3"
> > > > > > FT CDS 1..546
> > > > > > FT /gene="ARC21"
> > > > > > FT /note="actin-binding protein; ARPC3 21 kDa;
> > > > > > putative
> > > > > > FT member of Arp2/3 complex"
> > > > > > FT /codon_start=1
> > > > > > FT /product="actin-related protein 3"
> > > > > > FT /protein_id="ABF13401.1"
> > > > > > FT /db_xref="GI:93360014"
> > > > > > FT
> > > > > > /translation="MHSRWNGYEESSLLGCGVYPLRRTSRLTPPGPAPRMDEMIEEG
> > > > > > FT
> > > > > > EEEPQDIVDEAFYFFKPHMFFRNFPIKGAGDRVILYLTMYLHECLKKIVQLKREEAH
> > > > > > FT
> > > > > > SVLLNYATMPFASPGEKDFPFNAFFPAGNEEEQEKWREYAKQLRLEANARLIEKVFL
> > > > > > FT FPEKDGTGNKFWMAFAKRPFLASS"
> > > > > > atgcacagca ggtggaatgg gtatgaagaa agtagtcttt tgggctgcgg
> > > > > > tgtttatccg 60
> > > > > > cttcgccgca cgtcacggct cactccaccc ggccctgcac cgcggatgga
> > > > > > tgaaatgatt 120
> > > > > > gaggagggcg aagaggagcc acaagacatt gttgacgagg cattttactt
> > > > > > ttttaagccc 180
> > > > > > cacatgtttt ttcgtaattt tcccattaag ggtgctggtg atcgtgtcat
> > > > > > tctgtacttg 240
> > > > > > acgatgtacc ttcatgagtg tttgaagaaa attgtccagt tgaagcgtga
> > > > > > agaggcccat 300
> > > > > > tctgtgcttc ttaactacgc tacgatgccg tttgcatcac caggggaaaa
> > > > > > ggactttccg 360
> > > > > > tttaacgcgt ttttccctgc tgggaatgag gaggaacaag aaaaatggcg
> > > > > > agagtatgca 420
> > > > > > aaacagcttc gattggaggc caacgcacgt ctcattgaga aggtttttct
> > > > > > ttttccagag 480
> > > > > > aaggacggca ccggaaacaa gttctggatg gcgtttgcga agaggccttt
> > > > > > cttggcttct 540
> > > > > > agttag
> > > > > > 546
> > > > > > //
> > > > > > ID DQ472185 standard; DNA; INV; 543 BP.
> > > > > > XX
> > > > > > AC DQ472185;
> > > > > > XX
> > > > > > SV DQ472185.1
> > > > > > DT 15-MAY-2006
> > > > > > XX
> > > > > > DE Trypanosoma cruzi strain CL Brener actin-related protein 4
> > > > > > (ARC20) gene,
> > > > > > DE complete cds.
> > > > > > XX
> > > > > > KW .
> > > > > > XX
> > > > > > OS Trypanosoma cruzi strain CL Brener
> > > > > > OC Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
> > > > > > Trypanosoma;
> > > > > > OC Schizotrypanum.
> > > > > > XX
> > > > > > RN [1]
> > > > > > RP 1-543
> > > > > > RA De Melo L.D.B.;
> > > > > > RT "Actin of Trypanosoma cruzi: ubiquitous actin-binding
> > > > > > proteins";
> > > > > > RL Unpublished.
> > > > > > XX
> > > > > > RN [2]
> > > > > > RP 1-543
> > > > > > RA De Melo L.D.B.;
> > > > > > RT ;
> > > > > > RL Submitted (03-APR-2006) to the EMBL/GenBank/DDBJ databases.
> > > > > > RL Instituto de Biofisica Carlos Chagas Filho, Universidade
> > > > > > Federal do Rio
> > > > > > RL de Janeiro, Cidade Universitaria, CCS, Bl.G, Sl.G157, Rio de
> > > > > > Janeiro, RJ
> > > > > > RL 21949-900, Brazil
> > > > > > XX
> > > > > > FH Key Location/Qualifiers
> > > > > > FH
> > > > > > FT source 1..543
> > > > > > FT /organism="Trypanosoma cruzi strain CL Brener"
> > > > > > FT /mol_type="genomic DNA"
> > > > > > FT /strain="CL Brener"
> > > > > > FT /db_xref="taxon:353153"
> > > > > > FT gene <1..>543
> > > > > > FT /gene="ARC20"
> > > > > > FT /note="TcARC20"
> > > > > > FT mRNA <1..>543
> > > > > > FT /gene="ARC20"
> > > > > > FT /product="actin-related protein 4"
> > > > > > FT CDS 1..543
> > > > > > FT /gene="ARC20"
> > > > > > FT /note="actin-binding protein; ARPC4 20 kDa;
> > > > > > putative
> > > > > > FT member of Arp2/3 complex"
> > > > > > FT /codon_start=1
> > > > > > FT /product="actin-related protein 4"
> > > > > > FT /protein_id="ABF13402.1"
> > > > > > FT /db_xref="GI:93360016"
> > > > > > FT
> > > > > > /translation="MATAYLPYYDCIKCTLHAALCIGNYPSCTVERHNKPEVEVADH
> > > > > > FT
> > > > > > LENNGEIKVQDFLLNPIRIVRSEQESCLIEPSINSTRISVSFLKSDAIAEIIARKYV
> > > > > > FT
> > > > > > GFLAQRAKQFHILRKKPIPGYDISFLISHEEVETMHRNRIIQFIITFLMDIDADIAA
> > > > > > FT MKLNVNQRARRAAMEFFLALNFT"
> > > > > > atggcaaccg cctatttgcc ttactacgac tgcatcaagt gcacgttgca
> > > > > > cgcggctttg 60
> > > > > > tgcatcggga attatccttc atgtaccgtg gagcgtcata ataaaccaga
> > > > > > agttgaggtt 120
> > > > > > gcagaccatc tggagaataa tggtgaaata aaagtacaag atttccttct
> > > > > > taaccccata 180
> > > > > > cgcattgtgc gttcagaaca ggaaagttgt cttattgaac ctagtataaa
> > > > > > cagcacacgc 240
> > > > > > atatctgtat cgtttctcaa gagcgacgct attgcagaga ttattgcccg
> > > > > > aaagtacgtt 300
> > > > > > ggatttttag ctcagcgagc caaacagttt cacatcttga gaaaaaagcc
> > > > > > tattccggga 360
> > > > > > tatgatataa gttttttgat ttctcacgag gaagtagaaa caatgcatag
> > > > > > gaataggatt 420
> > > > > > attcaattta taattacttt cttgatggat attgatgctg acattgctgc
> > > > > > aatgaagttg 480
> > > > > > aatgtgaatc aacgtgcacg tcgagcagcg atggaattct ttcttgcatt
> > > > > > gaatttcaca 540
> > > > > > tga
> > > > > > 543
> > > > > > //
> > > > > > -----------------------------------------------------------------------
> > > > > > I get an exception message "Could Not Read Sequence". Same thing
> > > > > > happens if I use the readINSDSetDNA reader instead of readEMBLDNA
> > > > > > one
> > > > > > with the following INSDset file (beginning of the file):
> > > > > >
> > > > > > <?xml version="1.0"?>
> > > > > > <!DOCTYPE INSDSeq PUBLIC "-//NCBI//INSD INSDSeq/EN"
> > > > > > "INSD_INSDSeq.dtd">
> > > > > > <INSDSeq>
> > > > > > <INSDSeq_locus>DQ022078</INSDSeq_locus>
> > > > > > <INSDSeq_length>16729</INSDSeq_length>
> > > > > > <INSDSeq_moltype>DNA</INSDSeq_moltype>
> > > > > > <INSDSeq_topology>linear</INSDSeq_topology>
> > > > > > <INSDSeq_division>ENV</INSDSeq_division>
> > > > > > <INSDSeq_update-date>15-MAY-2006</INSDSeq_update-date>
> > > > > > <INSDSeq_create-date>15-MAY-2006</INSDSeq_create-date>
> > > > > > <INSDSeq_definition>Uncultured bacterium WWRS-2005 putative
> > > > > > aminoglycoside phosphotransferase (a3.001), putative oxidoreductase
> > > > > > (a3.002), putative oxidoreductase (a3.003), putative beta-lactamase
> > > > > > class C (estA3), putative permease (a3.005), putative transmembrane
> > > > > > signal peptide (a3.006), thiol-disulfide isomerase (a3.007), histone
> > > > > > acetyltransferase HPA2 (a3.008), putative enzyme (a3.009), putative
> > > > > > asparaginase (a3.010), hypothetical protein (a3.011), hypothetical
> > > > > > protein (a3.012), putative membrane protease subunit (a3.013),
> > > > > > putative haloalkane dehalogenase (a3.014), putative transcriptional
> > > > > > regulator (a3.015), putative peptidyl-dipeptidase Dcp (a3.016), and
> > > > > > hypothetical protein (a3.017) genes, complete
> > > > > > cds</INSDSeq_definition>
> > > > > > <INSDSeq_primary-accession>DQ022078</INSDSeq_primary-accession>
> > > > > > <INSDSeq_other-seqids>
> > > > > > <INSDSeqid>gb|DQ022078.1|</INSDSeqid>
> > > > > > <INSDSeqid>gi|71842722</INSDSeqid>
> > > > > > </INSDSeq_other-seqids>
> > > > > > <INSDSeq_keywords>
> > > > > > <INSDKeyword>ENV</INSDKeyword>
> > > > > > </INSDSeq_keywords>
> > > > > > <INSDSeq_references>
> > > > > > <INSDReference>
> > > > > > <INSDReference_reference>?</INSDReference_reference>
> > > > > > <INSDReference_position>1..16729</INSDReference_position>
> > > > > > <INSDReference_authors>
> > > > > > <INSDAuthor>Schmeisser,C.</INSDAuthor>
> > > > > > <INSDAuthor>Elend,C.</INSDAuthor>
> > > > > > <INSDAuthor>Streit,W.R.</INSDAuthor>
> > > > > > </INSDReference_authors>
> > > > > > <INSDReference_title>Isolation and biochemical
> > > > > > characterization
> > > > > > of two novel metagenome derived esterases</INSDReference_title>
> > > > > > <INSDReference_journal>Appl. Environ. Microbiol. 0:0-0
> > > > > > (2006)</INSDReference_journal>
> > > > > > </INSDReference>
> > > > > > <INSDReference>
> > > > > > <INSDReference_reference>?</INSDReference_reference>
> > > > > > <INSDReference_position>1..16729</INSDReference_position>
> > > > > > <INSDReference_authors>
> > > > > > <INSDAuthor>Schmeisser,C.</INSDAuthor>
> > > > > > <INSDAuthor>Elend,C.</INSDAuthor>
> > > > > > <INSDAuthor>Streit,W.R.</INSDAuthor>
> > > > > > </INSDReference_authors>
> > > > > > <INSDReference_journal>Submitted (29-APR-2005) to the
> > > > > > EMBL/GenBank/DDBJ databases. Molekulare Enzymtechnologie, University
> > > > > > Duisburg-Essen, Lotharstrasse 1, Duisburg D-47057,
> > > > > > Germany</INSDReference_journal>
> > > > > > </INSDReference>
> > > > > > </INSDSeq_references>
> > > > > >
> > > > > > So my question is wether the ASN2GB produces output that's
> > > > > > incompatible with BioJava parsers or is there a problem with the
> > > > > > sequence themselves or the problems with the majority of parsers???
> > > > > > Could it be that I'm using the API wrongly for the above formats,
> > > > > > although GenBank parser works as advertised with some exceptions
> > > > > > below:
> > > > > >
> > > > > > ISSUE #2:
> > > > > > When I try to parse GenBank files using the following code:
> > > > > >
> > > > > > BufferedReader inBuf = new BufferedReader(new
> > > > > > FileReader("genbank_output.gb"));
> > > > > > Namespace gbNspace = (Namespace)
> > > > > > RichObjectFactory.getObject(SimpleNamespace.class, new
> > > > > > Object[]{"gbSpace"} );
> > > > > > RichSequenceIterator gbSeqs =
> > > > > > RichSequence.IOTools.readGenbankDNA(inBuf,gbNspace);
> > > > > > while (gbSeqs.hasNext()) {
> > > > > > try {
> > > > > > RichSequence rs = gbSeqs.nextRichSequence();
> > > > > > // Further processing or RichSequence object from here
> > > > > >
> > > > > > } catch (BioException be){
> > > > > > be.printStackTrace();
> > > > > > }
> > > > > > }
> > > > > >
> > > > > > Genbank file in question:
> > > > > >
> > > > > > LOCUS BC074905 838 bp mRNA linear PRI
> > > > > > 15-APR-2006
> > > > > > DEFINITION Homo sapiens kallikrein 14, mRNA (cDNA clone MGC:104038
> > > > > > IMAGE:30915482), complete cds.
> > > > > > ACCESSION BC074905
> > > > > > VERSION BC074905.2 GI:50959825
> > > > > > KEYWORDS MGC.
> > > > > > SOURCE Homo sapiens (human)
> > > > > > ORGANISM Homo sapiens
> > > > > > Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
> > > > > > Euteleostomi;
> > > > > > Mammalia; Eutheria; Euarchontoglires; Primates;
> > > > > > Haplorrhini;
> > > > > > Catarrhini; Hominidae; Homo.
> > > > > > REFERENCE 1 (bases 1 to 838)
> > > > > > AUTHORS Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G.,
> > > > > > Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M.,
> > > > > > Schuler,G.D.,
> > > > > > Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F.,
> > > > > > Bhat,N.K.,
> > > > > > Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J.,
> > > > > > Hsieh,F.,
> > > > > > Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M.,
> > > > > > Hong,L.,
> > > > > > Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L.,
> > > > > > Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S.,
> > > > > > Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A.,
> > > > > > Peters,G.J.,
> > > > > > Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J.,
> > > > > > McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S.,
> > > > > > Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W.,
> > > > > > Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X.,
> > > > > > Gibbs,R.A.,
> > > > > > Fahey,J., Helton,E., Ketteman,M., Madan,A.,
> > > > > > Rodrigues,S.,
> > > > > > Sanchez,A., Whiting,M., Madan,A., Young,A.C.,
> > > > > > Shevchenko,Y.,
> > > > > > Bouffard,G.G., Blakesley,R.W., Touchman,J.W.,
> > > > > > Green,E.D.,
> > > > > > Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J.,
> > > > > > Myers,R.M.,
> > > > > > Butterfield,Y.S., Krzywinski,M.I., Skalska,U.,
> > > > > > Smailus,D.E.,
> > > > > > Schnerch,A., Schein,J.E., Jones,S.J. and Marra,M.A.
> > > > > > CONSRTM Mammalian Gene Collection Program Team
> > > > > > TITLE Generation and initial analysis of more than 15,000
> > > > > > full-length
> > > > > > human and mouse cDNA sequences
> > > > > > JOURNAL Proc. Natl. Acad. Sci. U.S.A. 99 (26), 16899-16903
> > > > > > (2002)
> > > > > > PUBMED 12477932
> > > > > > REFERENCE 2 (bases 1 to 838)
> > > > > > CONSRTM NIH MGC Project
> > > > > > TITLE Direct Submission
> > > > > > JOURNAL Submitted (25-JUN-2004) National Institutes of Health,
> > > > > > Mammalian
> > > > > > Gene Collection (MGC), Bethesda, MD 20892-2590, USA
> > > > > > REMARK NIH-MGC Project URL: http://mgc.nci.nih.gov
> > > > > > COMMENT On Aug 4, 2004 this sequence version replaced
> > > > > > gi:49901832.
> > > > > > Contact: MGC help desk
> > > > > > Email: [EMAIL PROTECTED]
> > > > > > Tissue Procurement: Genome Sequence Centre, British
> > > > > > Columbia Cancer
> > > > > > Center
> > > > > > cDNA Library Preparation: British Columbia Cancer
> > > > > > Research Center
> > > > > > cDNA Library Arrayed by: The I.M.A.G.E. Consortium
> > > > > > (LLNL)
> > > > > > DNA Sequencing by: Genome Sequence Centre,
> > > > > > BC Cancer Agency, Vancouver, BC, Canada
> > > > > > [EMAIL PROTECTED]
> > > > > > Martin Hirst, Thomas Zeng, Ryan Morin, Michelle Moksa,
> > > > > > Johnson
> > > > > > Pang, Diana Mah, Jing Wang, Kieth Fichter, Eric Chuah,
> > > > > > Allen
> > > > > > Delaney, Rob Kirkpatrick, Agnes Baross, Sarah Barber,
> > > > > > Mabel
> > > > > > Brown-John, Steve S. Chand, William Chow, Ryan
> > > > > > Babakaiff, Dave
> > > > > > Wong, Corey Matsuo, Jaclyn Beland, Susan Gibson, Luis
> > > > > > delRio, Ruth
> > > > > > Featherstone, Malachi Griffith, Obi Griffith, Ran Guin,
> > > > > > Nancy Liao,
> > > > > > Kim MacDonald, Mike R. Mayo, Josh Moran, Diana
> > > > > > Palmquist, JR
> > > > > > Santos, Duane Smailus, Jeff Stott, Miranda Tsai, George
> > > > > > Yang,
> > > > > > Jacquie Schein, Asim Siddiqui,Steven Jones, Rob Holt,
> > > > > > Marco Marra.
> > > > > >
> > > > > > Clone distribution: MGC clone distribution information
> > > > > > can be found
> > > > > > through the I.M.A.G.E. Consortium/LLNL at:
> > > > > > http://image.llnl.gov
> > > > > > Series: IRBU Plate: 4 Row: C Column: 3.
> > > > > >
> > > > > > Differences found between this sequence and the human
> > > > > > reference
> > > > > > genome (build 36) are described in misc_difference
> > > > > > features below.
> > > > > > FEATURES Location/Qualifiers
> > > > > > source 1..838
> > > > > > /organism="Homo sapiens"
> > > > > > /mol_type="mRNA"
> > > > > > /db_xref="taxon:9606"
> > > > > > /clone="MGC:104038 IMAGE:30915482"
> > > > > > /tissue_type="Lung, PCR rescued clones"
> > > > > > /clone_lib="NIH_MGC_273"
> > > > > > /lab_host="DH10B"
> > > > > > /note="Vector: pCR4 Topo TA with reversed
> > > > > > insert"
> > > > > > gene 1..838
> > > > > > /gene="KLK14"
> > > > > > /note="synonym: KLK-L6"
> > > > > > /db_xref="GeneID:43847"
> > > > > > /db_xref="HGNC:6362"
> > > > > > /db_xref="IMGT/GENE-DB:6362"
> > > > > > /db_xref="MIM:606135"
> > > > > > CDS 49..804
> > > > > > /gene="KLK14"
> > > > > > /codon_start=1
> > > > > > /product="KLK14 protein"
> > > > > > /protein_id="AAH74905.1"
> > > > > > /db_xref="GI:50959826"
> > > > > > /db_xref="GeneID:43847"
> > > > > > /db_xref="HGNC:6362"
> > > > > > /db_xref="IMGT/GENE-DB:6362"
> > > > > > /db_xref="MIM:606135"
> > > > > >
> > > > > > /translation="MFLLLTALQVLAIAMTRSQEDENKIIGGYTCTRSSQPWQAALLA
> > > > > >
> > > > > > GPRRRFLCGGALLSGQWVITAAHCGRPILQVALGKHNLRRWEATQQVLRVVRQVTHPN
> > > > > >
> > > > > > YNSRTHDNDLMLLQLQQPARIGRAVRPIEVTQACASPGTSCRVSGWGTISSPIARYPA
> > > > > >
> > > > > > SLQCVNINISPDEVCQKAYPRTITPGMVCAGVPQGGKDSCQGDSGGPLVCRGQLQGLV
> > > > > > SWGMERCALPGYPGVYTNLCKYRSWIEETMRDK"
> > > > > > misc_difference 98
> > > > > > /gene="KLK14"
> > > > > > /note="'G' in cDNA is 'A' in the human genome;
> > > > > > amino acid
> > > > > > difference: 'R' in cDNA, 'Q' in the human
> > > > > > genome."
> > > > > > misc_difference 133
> > > > > > /gene="KLK14"
> > > > > > /note="'T' in cDNA is 'C' in the human genome;
> > > > > > amino acid
> > > > > > difference: 'Y' in cDNA, 'H' in the human
> > > > > > genome."
> > > > > > ORIGIN
> > > > > > 1 atgtccctga gggtcttggg ctctgggacc tggccctcag cccctaaaat
> > > > > > gttcctcctg
> > > > > > 61 ctgacagcac ttcaagtcct ggctatagcc atgacacgga gccaagagga
> > > > > > tgagaacaag
> > > > > > 121 ataattggtg gctatacgtg cacccggagc tcccagccgt ggcaggcggc
> > > > > > cctgctggcg
> > > > > > 181 ggtcccaggc gccgcttcct ctgcggaggc gccctgcttt caggccagtg
> > > > > > ggtcatcact
> > > > > > 241 gctgctcact gcggccgccc gatccttcag gttgccctgg gcaagcacaa
> > > > > > cctgaggagg
> > > > > > 301 tgggaggcca cccagcaggt gctgcgcgtg gttcgtcagg tgacgcaccc
> > > > > > caactacaac
> > > > > > 361 tcccggaccc acgacaacga cctcatgctg ctgcagctac agcagcccgc
> > > > > > acggatcggg
> > > > > > 421 agggcagtca ggcccattga ggtcacccag gcctgtgcca gccccgggac
> > > > > > ctcctgccga
> > > > > > 481 gtgtcaggct ggggaactat atccagcccc atcgccaggt accccgcctc
> > > > > > tctgcaatgc
> > > > > > 541 gtgaacatca acatctcccc ggatgaggtg tgccagaagg cctatcctag
> > > > > > aaccatcacg
> > > > > > 601 cctggcatgg tctgtgcagg agttccccag ggcgggaagg actcttgtca
> > > > > > gggtgactct
> > > > > > 661 gggggacccc tggtgtgcag aggacagctc cagggcctcg tgtcttgggg
> > > > > > aatggagcgc
> > > > > > 721 tgcgccctgc ctggctaccc cggtgtctac accaacctgt gcaagtacag
> > > > > > aagctggatt
> > > > > > 781 gaggaaacga tgcgggacaa atgatggtct tcacggtggg atggacctcg
> > > > > > tcagctgc
> > > > > > //
> > > > > >
> > > > > > I get the following exception:
> > > > > >
> > > > > > java.lang.IllegalArgumentException: Authors string cannot be null
> > > > > > org.biojava.bio.BioException: Could not read sequence
> > > > > > at
> > > > > > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
> > > > > > at
> > > > > > exonhit.parsers.GenBankParser.getSequences(GenBankParser.java:107)
> > > > > > at
> > > > > > exonhit.parsers.GenBankParser.runGBparser(GenBankParser.java:258)
> > > > > > at
> > > > > > exonhit.parsers.GenBankParser.main(GenBankParser.java:341)
> > > > > > Caused by: java.lang.IllegalArgumentException: Authors string
> > > > > > cannot be null
> > > > > > at
> > > > > > org.biojavax.DocRefAuthor$Tools.parseAuthorString(DocRefAuthor.java:76)
> > > > > > at
> > > > > > org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:356)
> > > > > > at
> > > > > > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
> > > > > >
> > > > > > -----------------------------------------------------------------------
> > > > > >
> > > > > > I'm trying to see what could be the problem with this particular
> > > > > > sequence. Looks to me like the AUTHORS portion is not getting
> > > > > > parsed
> > > > > > correctly. Any ideas would be greatly appreciated!
> > > > > >
> > > > > --
> > > > > Richard Holland (BioMart Team)
> > > > > EMBL-EBI
> > > > > Wellcome Trust Genome Campus
> > > > > Hinxton
> > > > > Cambridge CB10 1SD
> > > > > UNITED KINGDOM
> > > > > Tel: +44-(0)1223-494416
> > > > >
> > > > >
> > > >
> > > >
> > > --
> > > Richard Holland (BioMart Team)
> > > EMBL-EBI
> > > Wellcome Trust Genome Campus
> > > Hinxton
> > > Cambridge CB10 1SD
> > > UNITED KINGDOM
> > > Tel: +44-(0)1223-494416
> > >
> > >
> >
> >
> --
> Richard Holland (BioMart Team)
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> UNITED KINGDOM
> Tel: +44-(0)1223-494416
>
>
--
Best Regards,
Seth Johnson
Senior Bioinformatics Associate
Ph: (202) 470-0900
Fx: (775) 251-0358
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