Hi Alexander, There are two issues here. Firstly, the genbank parser was not grasefully handeling blanks lines (hence the index out of bounds error - it was trying to index a char not in the line). Seccondly, your genbank file has some traling text (after the ///) that states an update date, and this is not part of a valid genbank entry.
I've commited the blank-line fix to cvs. I guess you need to trimm the spurious lines from your Genbank entries. Did they come from a script? Matthew Alexander Churbanov wrote: > Hi Mtthew, > > Thanks for your willing to help me. > The accession number is AF207834 at NCBI GenBank. > I am sending you the picture of what I got. Sorry, > I don't know yet how to create error log files in > Java. > I run exactly the file from your demo folder on the > mRNA flat file. > Most probably I do something stupid - I do not have > experience working with your framework. > > Thanks, > > Alexander > > --- Matthew Pocock <[EMAIL PROTECTED]> wrote: > >>Mark: Do RNA Genbank entries use agcu? RNA embl >>entries use DNA (agct) >>to serialise the sequence. >> >>Alexander: Could you give us an accession number >>that causes this error >>as well as the error you get? The complete stack >>trace is always helpful >>for fixing things. >> >>Matthew >> >>Schreiber, Mark wrote: >> >>>The problem is probably being caused by the use of >> >>the DNA alphabet >> >>>instead of the RNA alpahbet. Are you getting >> >>IllegalSymbolExceptions? >> >>>If this is the case you need to use the RNA >> >>alphabet in the GenBank >> >>>parser this can be found by calling >> >>RNATools.getRNA(); >> >>>- Mark >>> >>> >>> >>>>-----Original Message----- >>>>From: Alexander Churbanov >>> >>[mailto:[EMAIL PROTECTED]] >> >>>>Sent: Thursday, 16 May 2002 1:56 p.m. >>>>To: [EMAIL PROTECTED] >>>>Subject: [Biojava-l] parsing mRNA GenBank flat >>> >>file >> >>>> >>>> Hello, >>>> >>>> I am trying to parse mRNA file from Gen Bank >>> >>using >> >>>>your demo program (That parses DNA GenBank flat >>> >>file). >> >>>>It crashes on the halfway or at the beginning. Do >>> >>you >> >>>>have any suggestions, other methods, demo programs >>> >>or >> >>>>other sources showing how to do it. >>>> Thanks in advance, >>>> >>>> Alexander Tchourbanov >>>> >>>>__________________________________________________ >>>>Do You Yahoo!? >>>>LAUNCH - Your Yahoo! Music Experience >>>>http://launch.yahoo.com >>>>_______________________________________________ >>>>Biojava-l mailing list - [EMAIL PROTECTED] >>>>http://biojava.org/mailman/listinfo/biojava-l >>>> >>> >>> > ======================================================================= > >>>Attention: The information contained in this >> >>message and/or attachments >> >>>from AgResearch Limited is intended only for the >> >>persons or entities >> >>>to which it is addressed and may contain >> >>confidential and/or privileged >> >>>material. Any review, retransmission, >> >>dissemination or other use of, or >> >>>taking of any action in reliance upon, this >> >>information by persons or >> >>>entities other than the intended recipients is >> >>prohibited by AgResearch >> >>>Limited. If you have received this message in >> >>error, please notify the >> >>>sender immediately. >>> >> > ======================================================================= > >>>_______________________________________________ >>>Biojava-l mailing list - [EMAIL PROTECTED] >>>http://biojava.org/mailman/listinfo/biojava-l >>> >> >> >> > > > __________________________________________________ > Do You Yahoo!? > LAUNCH - Your Yahoo! Music Experience > http://launch.yahoo.com > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > LOCUS AF207834 600 bp mRNA linear PRI 02-NOV-2001 > DEFINITION Macaca mulatta epididymis-specific protein ESP13.6 mRNA, complete > cds. > ACCESSION AF207834 > VERSION AF207834.1 GI:16588332 > KEYWORDS . > SOURCE rhesus monkey. > ORGANISM Macaca mulatta > Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; > Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; > Cercopithecinae; Macaca. > REFERENCE 1 (bases 1 to 600) > AUTHORS Liu,Q., Hamil,K.G., Sivashanmugam,P., Grossman,G., > Soundararajan,R., Rao,A.J., Richardson,R.T., Zhang,Y.L., > O'Rand,M.G., Petrusz,P., French,F.S. and Hall,S.H. > TITLE Primate epididymis-specific proteins: characterization of ESC42, a > novel protein containing a trefoil-like motif in monkey and human > JOURNAL Endocrinology 142 (10), 4529-4539 (2001) > MEDLINE 21448442 > PUBMED 11564719 > REFERENCE 2 (bases 1 to 600) > AUTHORS Liu,Q., Hamil,K.G., Johnson,R.T. Jr., Zhang,Y.L., French,F.S. and > Hall,S.H. > TITLE Direct Submission > JOURNAL Submitted (23-NOV-1999) Pediatrics, The Laboratories for > Reproductive Biology, The University of North Carolina, Room 382, > MSRB, CB#7500, Chapel Hill, NC 27599-7500, USA > FEATURES Location/Qualifiers > source 1..600 > /organism="Macaca mulatta" > /db_xref="taxon:9544" > CDS 27..398 > /codon_start=1 > /product="epididymis-specific protein ESP13.6" > /protein_id="AAL26779.1" > /db_xref="GI:16588333" > /translation="MKLLLLALPILVLLPQVIPAYGGEKKCWNRSGHCRKQCKDGEAV > KETCKNHRACCVPSNEDHRRLPTTSPTPLSDSTPGIIDNILTIRFTTDYFEISSKKDM > VEESEAGQGTQTSPPNVHHTS" > BASE COUNT 205 a 151 c 100 g 144 t > ORIGIN > 1 ctaccatctc ctgtttccca agcaccatga aactcctgct gttggctctt cctatccttg > 61 tgctcctacc ccaagtgatc ccagcctatg gtggtgaaaa aaaatgctgg aacagatcag > 121 ggcactgcag gaaacaatgc aaagatggag aagcagtgaa agaaacatgc aaaaatcatc > 181 gagcctgctg cgttccatct aatgaagacc acaggcgact tcctacgaca tctcccacac > 241 ccttgagtga ctcaacacca ggaattattg ataatatttt aacaataagg ttcactacag > 301 actactttga aataagcagc aagaaagaca tggttgaaga gtctgaggcg ggacagggaa > 361 ctcagacctc tcccccaaat gttcaccata cctcatgact tcttctcgaa tgtcactcac > 421 ccctgtcctc agagtgataa actaagtcac atacatatag ataaaacacc acagtgacct > 481 cccacttccc accaatatgt aattctatta atagaaacag ctgtgtaaag aagtctaaaa > 541 ttttcactat ttccaatgat aaactcttca gtgctcttct tgaaaaaaaa aaaaaaaaaa > // > > > > Revised: October 24, 2001. > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
