Thanks for the extra info. 2008/10/1 David Toomey <[EMAIL PROTECTED]>: > They are on the same OS. For all my tests I have run the blast search and > parsing on the same OS. This has mostly been windows but I have also tried > the whole thing on Linux and I get the same problem. > I have done some more testing and I don't think the carriage return is the > problem. > What I have found is that if the second line is less than 11 characters the > error is thrown. If I add 4 spaces in front of the 'GN=ISPF' on the second > line then it is parsed correctly, like this. > > 2,4-cyclodiphosphate synthase OS=Plasmodium falciparum (isolate 3D7) > GN=ISPF > > I haven't figured out why it parses correctly when it is the only entry in > the file, even without the spaces. So maybe I am still missing something. > > Cheers, > > Dave > > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf > Of Richard Holland > Sent: 30 September 2008 17:31 > To: David Toomey > Cc: biojava-l@lists.open-bio.org > Subject: Re: [Biojava-l] StringIndexOutOfBoundsException while parsing blast > result > > Sounds like it _might_ be something to do with the carriage return > itself. Is the blast file generated on the same OS that you're running > your analysis on? (e.g. you might run Blast on a Linux box, but > attempt to parse the file on a Windows box?). If the two OSes are > different, this might point to it - as Linux won't necessarily > understand the Windows linebreaks, or vice versa, and might > misinterpret them. When you copy the portion of the file to a new file > on the OS you're running the analysis on, it will substitute its own > local linebreaks and thus mask the problem. > > So the first thing I'd check is to what the two OSes involved are. If > they're different, try running your analysis program on the same OS as > the Blast output was generated on. If that does fix it, then try > putting your Blast files through dos2unix or something similar to > convert the linebreaks before running your analysis program. > > If they're the same OS, then we still have a problem! > > cheers, > Richard > > > >
-- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: [EMAIL PROTECTED] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l
