[Biojava-l] [biojavax] EMBL parser error
Morgane THOMAS-CHOLLIER
mthomasc at vub.ac.be
Sat Apr 8 08:20:47 UTC 2006
It works fine now !
Thanks for your help,
cheers,
Morgane.
Richard Holland wrote:
>Hi. Someone else had checked in a change to a different class, but that
>change was incorrect and didn't compile. It should compile now.
>
>cheers,
>Richard
>
>PS. Note to all those who commit changes - PLEASE check your code
>compiles first before committing it!
>
>On Fri, 2006-04-07 at 15:07 +0200, Morgane THOMAS-CHOLLIER wrote:
>
>
>>I tried to checkout biojava-live but it seems I cannot build it anymore.
>>I get the following error :
>>
>>compile-biojava:
>> [javac] Compiling 1321 source files to
>>/Users/morgane/Documents/PHD/KermitDB/Kermit_workspace/biojava-live3/ant-build/classes/biojava
>> [javac]
>>/Users/morgane/Documents/PHD/KermitDB/Kermit_workspace/biojava-live3/src/org/biojavax/utils/StringTools.java:97:
>>exception java.io.IOException is never thrown in body of corresponding
>>try statement
>> [javac] } catch (IOException e) {
>> [javac] ^
>> [javac] Note: Some input files use or override a deprecated API.
>> [javac] Note: Recompile with -deprecation for details.
>> [javac] 1 error
>>
>>I use Mac OS X 10.3.9, java 1.4.2.
>>
>>Hope you could help,
>>
>>Cheers,
>>
>>Morgane.
>>
>>
>>Richard Holland wrote:
>>
>>
>>
>>>Sorry, my bad. An off-by-one error...
>>>
>>>Check it out again and see if it works now.
>>>
>>>cheers,
>>>Richard
>>>
>>>PS. I don't have any EMBL files to test with at the moment otherwise I'd
>>>check it myself... :)
>>>
>>>
>>>On Fri, 2006-04-07 at 14:18 +0200, Morgane THOMAS-CHOLLIER wrote:
>>>
>>>
>>>
>>>
>>>>I now get another error message with the same file :
>>>>
>>>>Exception in thread "main" org.biojava.bio.BioException: Could not read
>>>>sequence
>>>> at
>>>>org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111)
>>>> at
>>>>org.embnet.be.biojavax.tryout.EMBLParseTest.main(EMBLParseTest.java:34)
>>>>Caused by: java.lang.IndexOutOfBoundsException: No group 5
>>>> at java.util.regex.Matcher.group(Matcher.java:355)
>>>> at
>>>>org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:271)
>>>> at
>>>>org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108)
>>>> ... 1 more
>>>>
>>>>Here is the complete file, for info:
>>>>
>>>>ID DQ158013 standard; genomic DNA; VRT; 118 BP.
>>>>XX
>>>>AC DQ158013;
>>>>XX
>>>>SV DQ158013.1
>>>>XX
>>>>DT 19-JAN-2006 (Rel. 86, Created)
>>>>DT 19-JAN-2006 (Rel. 86, Last updated, Version 1)
>>>>XX
>>>>DE Triturus helveticus clone Thel.b9 HOXB9 (Hoxb9) gene, partial cds.
>>>>XX
>>>>KW .
>>>>XX
>>>>OS Triturus helveticus (palmate newt)
>>>>OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
>>>>Amphibia;
>>>>OC Batrachia; Caudata; Salamandroidea; Salamandridae; Triturus.
>>>>XX
>>>>RN [1]
>>>>RP 1-118
>>>>RX DOI; 10.1016/j.ympev.2005.08.012.
>>>>RX PUBMED; 16198128.
>>>>RA Mannaert A., Roelants K., Bossuyt F., Leyns L.;
>>>>RT "A PCR survey for posterior Hox genes in amphibians";
>>>>RL Mol. Phylogenet. Evol. 38(2):449-458(2006).
>>>>XX
>>>>RN [2]
>>>>RP 1-118
>>>>RA Mannaert A., Roelants K., Bossuyt F., Leyns L.;
>>>>RT ;
>>>>RL Submitted (09-AUG-2005) to the EMBL/GenBank/DDBJ databases.
>>>>RL Biology Department, Vrije Universiteit Brussel, Pleinlaan 2,
>>>>Brussels 1050,
>>>>RL Belgium
>>>>XX
>>>>FH Key Location/Qualifiers
>>>>FH
>>>>FT source 1..118
>>>>FT /organism="Triturus helveticus"
>>>>FT /mol_type="genomic DNA"
>>>>FT /clone="Thel.b9"
>>>>FT /db_xref="taxon:256425"
>>>>FT gene <1..>118
>>>>FT /gene="Hoxb9"
>>>>FT /note="Hoxb-9"
>>>>FT mRNA <1..>118
>>>>FT /gene="Hoxb9"
>>>>FT /product="HOXB9"
>>>>FT CDS <1..>118
>>>>FT /codon_start=2
>>>>FT /gene="Hoxb9"
>>>>FT /product="HOXB9"
>>>>FT /db_xref="UniProtKB/TrEMBL:Q2LK47"
>>>>FT /protein_id="ABA39736.1"
>>>>FT /translation="KYQTLELEKEFLFNMYLTRDRRHEVARLLNLSERQVKIW"
>>>>XX
>>>>SQ Sequence 118 BP; 28 A; 35 C; 37 G; 18 T; 0 other;
>>>> caaataccag acgctggagc tggagaagga gttcctgttc aacatgtacc
>>>>tcacccggga 60
>>>> ccgcaggcac gaggtggccc ggctgctgaa cctcagcgag cgccaggtca
>>>>agatctgg 118
>>>>//
>>>>
>>>>Thanks for helping,
>>>>
>>>>Morgane.
>>>>
>>>>Richard Holland wrote:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>That was indeed a bug. I have made a change to the date parsing in
>>>>>EMBLFormat and committed it to CVS. Could you test it for me please?
>>>>>
>>>>>cheers,
>>>>>Richard
>>>>>
>>>>>On Fri, 2006-04-07 at 11:20 +0200, Morgane THOMAS-CHOLLIER wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>Hello,
>>>>>>
>>>>>>I am currently using biojavax that I checked out today from CVS to parse
>>>>>>an EMBL file, exported from EBI SRS server.
>>>>>>
>>>>>>I ran into this error :
>>>>>>
>>>>>>Exception in thread "main" org.biojava.bio.BioException: Could not read
>>>>>>sequence
>>>>>> at
>>>>>>org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111)
>>>>>> at
>>>>>>org.embnet.be.biojavax.tryout.EMBLParseTest.main(EMBLParseTest.java:34)
>>>>>>Caused by: org.biojava.bio.seq.io.ParseException: Bad date type found: 86
>>>>>> at
>>>>>>org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:278)
>>>>>> at
>>>>>>org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108)
>>>>>> ... 1 more
>>>>>>
>>>>>>The EMBL file is :
>>>>>>
>>>>>>ID DQ158013 standard; genomic DNA; VRT; 118 BP.
>>>>>>XX
>>>>>>AC DQ158013;
>>>>>>XX
>>>>>>SV DQ158013.1
>>>>>>XX
>>>>>>DT 19-JAN-2006 (Rel. 86, Created)
>>>>>>DT 19-JAN-2006 (Rel. 86, Last updated, Version 1)
>>>>>>XX
>>>>>>DE Triturus helveticus clone Thel.b9 HOXB9 (Hoxb9) gene, partial cds.
>>>>>>
>>>>>>Removing the two lines that comprise the date information resolves the
>>>>>>problem.
>>>>>>
>>>>>>Thanks,
>>>>>>
>>>>>>Morgane.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>--
>>>>**********************************************************
>>>>Morgane THOMAS-CHOLLIER, PHD Student
>>>>
>>>>Vrije Universiteit Brussels (VUB)
>>>>Laboratory of Cell Genetics
>>>>Pleinlaan 2
>>>>1050 Brussels
>>>>Belgium
>>>>
>>>>
>>>>
>>>>
>>>>
>>
>>
--
**********************************************************
Morgane THOMAS-CHOLLIER, PHD Student
Vrije Universiteit Brussels (VUB)
Laboratory of Cell Genetics
Pleinlaan 2
1050 Brussels
Belgium
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