[Biojava-l] bioJAVA bug??
christophe_pichon@eu.biomerieux.com
christophe_pichon@eu.biomerieux.com
Tue, 31 Oct 2000 08:36:28 +0100
Mr,
I have use a tutorial about bioJAVA on the web
(http://www.biojava.org/tutorials), but i have found a possible problem. I have
use the last java class of the chap1 tutorial (calc G+C contents), i have
replace the line :
StreamReader stream = new StreamReader(br,
new FastaFormat(),
dnaParser,
fact);
by this one :
StreamReader stream = new StreamReader(br,
new GenbankFormat(),
dnaParser,
fact);
and i run the class with a genbank file that contains many entry, one of them
have made an Exception :
java.lang.reflect.InvocationTargetException: org.biojava.bio.BioException: bad
locator: order order(463..471,481..489)
Personally, i think the genbank file have a problem of formatting with there
repeat_region flag.
The genbank file were this exception arrived is the following one (<<HERE is a
post error underline):
LOCUS AF145252 2769 bp DNA BCT 09-JUN-1999
DEFINITION Rhodothermus marinus heat shock protein GroES (groES) and heat
shock protein GroEL (groEL) genes, complete cds.
ACCESSION AF145252
VERSION AF145252.1 GI:5020008
KEYWORDS .
SOURCE Rhodothermus marinus.
ORGANISM Rhodothermus marinus
Bacteria; CFB group; Rhodothermus group; Rhodothermus.
REFERENCE 1 (bases 1 to 2769)
AUTHORS Thorolfsdottir,E.T.T., Backman,V.M., Blondal,T.,
Thorbjarnardottir,S.H., Palsdottir,A., Hauksdottir,H.,
Kristjansdottir,S. and Eggertsson,G.
TITLE Heat shock in Rhodothermus marinus: Cloning and sequence analysis
of the groESL, dnaK and dnaJ genes
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 2769)
AUTHORS Backman,V., Thorolfsdottir,E.T.T., Kristjansdottir,S.,
Thorbjarnardottir,S.H. and Eggertsson,G.
TITLE Direct Submission
JOURNAL Submitted (23-APR-1999) Laboratory of Molecular Genetics, Insitute
of Biology, Grensasvegur 12, Reykjavik 108, Iceland
FEATURES Location/Qualifiers
source 1..2769
/organism="Rhodothermus marinus"
/strain="ITI 376"
/db_xref="taxon:29549"
repeat_region order(463..471,481..489) <<<<<<<<<<<<<< HERE
/rpt_family="CIRCE"
/rpt_type=inverted
gene 568..870
/gene="groES"
CDS 568..870
/gene="groES"
/codon_start=1
/transl_table=11
/product="heat shock protein GroES"
/protein_id="AAD37975.1"
/db_xref="GI:5020009"
/translation="MAKVKIKPLSDRVVIKPEPPEEKTESGLYIPDTAKEKPQRGTVI
AVGPGRVENGTKIEMSVKEGDKVLYGKYAGTEITIDGEEYLIMRETDILGIIEEEK"
gene 954..2576
/gene="groEL"
CDS 954..2576
/gene="groEL"
/codon_start=1
/transl_table=11
/product="heat shock protein GroEL"
/protein_id="AAD37976.1"
/db_xref="GI:5020010"
/translation="MAAKQITFNADARMALKRGVDKLADAVKVTLGPKGRNVIIEKKF
GAPTVTKDGVTVAKEIELEDKLENVGAQMVKEVASKTSDVAGDGTTTATVLAQAILTA
GLKSVTAGANPMDLKRGIDKAVEVVVAELRKMSQEVQDKNRIAQVATISANGDKAIGQ
LIADAFEKVGKDGVITVEEAKGTETTLEVVEGMQFDRGYLSPYFVTNPDTMEAVLEDA
YILIHDKKISAMKDLLPILEKVVQTGRPLLIIAEDVEGEALATLVVNKLRGVLKVAAV
KAPGFGDRRKAMLEDIAILTGGTVISEEKGYRLENATLDYLGQAERIIVDKDNTTIVG
GKGDPAQIKARANQIRQQIEETTSDYDREKLQERLAKLAGGVAVLKIGAATEPEMKEK
KARVEDALHATRAAVEEGIVPGGGVAYIRAIAALDKVEVENEDQKIGVQIVQRALEEP
LRQIAANAGWEGSIVVQRVKEGQGDFGFNAQTEEFGNLLEQGVIDPTKVARTALENAA
SVAGLLLTTEAVVAEKPEKEKAAAPSPGDMDF"
BASE COUNT 629 a 776 c 952 g 412 t
ORIGIN
1 tgcaggcccc agtccagcgc cggaggcaac agcgccccgc tcagtaccag aggcgcccgc
61 cggtaaatcc accgcgcccc gtcgccgagc agcggcagca gcagcgatcc cagaaaaagg
121 ccggtataga ttccatagca gcgctggcag acggccagct gaactccgtc gatccagaac
181 gaacggtcag gcaactggtg gcacaccggc gcgaaggccg ccatgagcaa cgcccggatc
241 gaaggcggca cgaacggcgg cagcgagatc agcagcagaa gcaggccggt gacgccggcc
301 gccagcagag gaacgcggga cgattgtaac gccatggtta taaaattgaa ggataaaccc
361 tgtgtccttt aaagctacac attctggccg ttctatgcca gtttgttttg agatttcttc
421 acggagggca ggaactcgcc cgaaaaacga tcggttgaag gcttagcact ctcgaaatga
481 gagtgctaac aaatcttgat caatccttaa aaatctgatc ggggttgctt catccaccaa
541 ccgtaaaaaa ccatggaggt gcgcgatatg gcgaaggtta aaattaagcc gctgagcgat
601 cgggttgtaa tcaagccgga gccgccggag gagaagaccg aaagcggtct gtacattccg
661 gacacggcca aggagaaacc gcagcggggt acggtgatcg ccgtcggtcc cgggcgtgtg
721 gagaacggga ccaagattga gatgagcgtg aaggagggcg acaaggtgct ctacggcaag
781 tatgccggca ccgagatcac gatcgacggc gaggagtatc tcatcatgcg ggagaccgac
841 atcctgggga ttatcgaaga ggagaagtaa gcgctgcgaa tcgttcgtgg cgcttttttc
901 gtgacccgtg gtccggaaac cggtgagctg aaaacaaacc tggagggaaa actatggctg
961 cgaagcagat tacgttcaac gcggatgcgc gcatggcgct gaagcggggc gtcgacaagc
1021 tggccgacgc tgtaaaggtg acgctggggc cgaagggccg caacgtgatc attgagaaga
1081 agtttggcgc cccgaccgtc acgaaggacg gcgtgacggt ggccaaggaa atcgagctgg
1141 aggacaagct ggagaacgtc ggtgcccaga tggtcaagga ggtcgcctcg aagacgagcg
1201 atgtggcggg tgacggtacg acgacggcga ccgtcctggc ccaggccatc ctgacggccg
1261 gtctgaagag cgtcacggcc ggtgcgaacc cgatggacct gaagcggggc atcgacaagg
1321 ccgtggaggt ggtcgtggcc gagctgcgca agatgagcca ggaggtgcag gacaagaacc
1381 gcattgcgca ggtggcgacg atctcggcca acggcgacaa ggccatcggg cagctcatcg
1441 ccgacgcgtt cgagaaggtc ggcaaggacg gcgtcatcac ggtcgaggag gccaagggca
1501 ccgagacgac gctcgaggtc gtcgagggta tgcagttcga ccgggggtac ctctcgccct
1561 acttcgtgac gaaccccgac acgatggagg ccgtcctgga ggacgcctac atcctgattc
1621 atgacaagaa gatctcggcg atgaaggacc tgctgccgat tctggagaag gtggtccaga
1681 ccggccggcc gctcctgatc atcgccgagg atgtggaggg cgaggcgctg gcgaccctgg
1741 tcgtcaacaa gctgcgcggc gtgctgaagg tggcggccgt caaggcgccg ggcttcggcg
1801 atcgccgcaa ggccatgctg gaagacatcg ccatcctgac cggcggtacg gttatctctg
1861 aggagaaggg ttaccgcctg gagaacgcca cgctggacta cctgggccag gccgagcgga
1921 tcatcgtcga caaggacaac acgacgatcg tcggcggcaa gggcgatccg gctcagatca
1981 aggcccgcgc caaccagatc cggcagcaga tcgaggagac caccagcgac tacgaccgcg
2041 agaagctgca ggagcggttg gcgaagctgg ccggtggcgt ggcggtactg aagatcggtg
2101 cggccaccga gcccgaaatg aaagagaaga aggcccgcgt cgaggacgcg ctgcacgcga
2161 cgcgtgccgc cgtcgaagag ggcatcgtgc cgggtggtgg tgtggcctac atccgggcca
2221 ttgcggcgct cgacaaggtc gaggtggaaa acgaggacca gaagatcggc gtgcagatcg
2281 tccagcgggc gctggaagag ccgctccggc agattgctgc gaacgcgggc tgggaaggct
2341 cgatcgtcgt ccagcgcgtc aaggaaggtc agggcgactt cggcttcaac gcccagaccg
2401 aagagttcgg taacctgctg gagcagggcg tgatcgaccc gacgaaggtc gcgcgcacgg
2461 cgctggagaa cgccgcctcg gtggccggcc tgctgctgac cacggaggcc gtcgtggccg
2521 aaaagccgga gaaggaaaag gctgcggcgc cgagccctgg cgacatggac ttctaagcgc
2581 gccctgacac acccccgcaa ccccgaagcg gggctgccac accggcagcc gttttttgtt
2641 acctgcacaa cattttgtct ggaagccgtg cggcctgtgg tcaggcgcga agcaagggcc
2701 cttctgcgta gcacttcgga tgacgcctcc gtggctttgc tacaacgcgt tcgtatcagc
2761 aaagcgtaa
//
Thanks, for paying attention of that.
M. Pichon Christophe