I'd love to see a proper solution to this that doesn't involve upping the read-ahead limit. I was aware that it might be the issue, but had no idea why it was not failing for other similar long sequences. I look forward to seeing your suggested fix!
thanks, Richard Josh Goodman wrote: > Hi Richard and JP, > > I think I can be of some help as I'm the FlyBase developer responsible for > generating these troublesome FASTA files :-). The cause of this problem > appears to be the description line length for the record FBpp0145470. > > The trouble lies in org.biojavax.bio.seq.io.FastaFormat in the while loop > at line 196. Biojava correctly reads in FBpp0145468 but throws an error > when trying to parse FBpp0145469. There is nothing wrong in FBpp0145469 > but when biojava reaches the end of the sequence it reads in the header > for the next record (FBpp0145470). It then tries to reset the > BufferedReader to the start of FBpp0145470 but that is where the exception > is thrown because line 197 sets the read ahead limit to 500 characters and > the reader.readLine() command exceeds that limit. > > What isn't obvious to me is why other large definition lines that precede > that line don't throw the same error (e.g. FBpp0157909). I guess the > javadoc on BufferedReader.mark() does say "may fail" but I assumed it > would be more predictable than that. > > The file in question can be downloaded from > ftp://ftp.flybase.net/genomes/Drosophila_grimshawi/dgri_r1.3_FB2008_07/fasta/dgri-all-translation-r1.3.fasta.gz. > > If there is interest in a solution that doesn't involve simply upping the > read ahead limit I can put a patch file together in the next day or so. > > Cheers, > Josh > > On Tue, 28 Apr 2009, Richard Holland wrote: > >> You're right, doesn't look like newlines. >> >> The "Mark invalid" happens when the parser looks too far ahead in the >> file attempting to seek out the next valid sequence to parse. I'm not >> sure why this is happening. >> >> I don't have the time to test right now but if you could post the link >> to where someone could download the same FASTA as you're using, then it >> would make it possible for someone else to investigate in more detail. >> >> thanks, >> Richard >> >> JP wrote: >>> Thanks Richard for your prompt reply. >>> >>> I will not attach the fasta file I am parsing (12MB) its >>> dgri-all-translation-r1.3.fasta from the flybase project. >>> >>> If the file had any extra new lines I would see them when I loaded it in >>> a text editor - no ? >>> >>> I implemented the whole thing without using Biojava (for this part) >>> >>> fr = new FileReader(fastaProteinFileName); >>> br = new BufferedReader(fr); >>> String fastaLine; >>> String startAccession = '>' + accessionId.trim(); >>> String fastaEntry = ""; >>> boolean record = false; >>> while ((fastaLine = br.readLine()) != null) { >>> fastaLine = fastaLine.trim() + '\n'; >>> if (fastaLine.startsWith(startAccession)) { >>> record = true; >>> } else if (record && fastaLine.startsWith(">")) { >>> record = false; >>> break; >>> } >>> if (record) { >>> fastaEntry += fastaLine; >>> } >>> } >>> >>> >>> Notice - I do not use regex - since I'd need to read the whole file and >>> then regex upon it (if the record is the first one - I just read that one). >>> >>> Cheers >>> JP >>> >>> >>> On Tue, Apr 28, 2009 at 3:27 PM, Richard Holland >>> <[email protected] <mailto:[email protected]>> wrote: >>> >>> The "Mark invalid" exception is indicating that the parser has gone too >>> far ahead in the file looking for a valid header. I'm not sure why but >>> looking at your original query, there may be extra newlines embedded >>> into your FASTA header line? That would definitely confuse it. >>> >>> The parser is not able to currently pull out just one sequence - in >>> effect this is a search facility, which it doesn't have. :( >>> >>> thanks, >>> Richard >>> >>> JP wrote: >>> > Hi all at BioJava, >>> > >>> > I am trying to parse several FASTA files using the following code: >>> > >>> > fr = new FileReader(fastaProteinFileName); >>> >> br = new BufferedReader(fr); >>> >> >>> >> RichSequenceIterator protIter = IOTools.readFastaProtein(br, null); >>> >> while (protIter.hasNext()) { >>> >> BioEntry bioEntry = protIter.nextBioEntry(); >>> >> System.out.println (fastaProteinFileName + " == " + >>> accessionId + " = >>> >> " + bioEntry.getAccession()); >>> >> } >>> > >>> > >>> > At particular points in my fasta file - I get the following exception: >>> > >>> > 14:53:42,546 ERROR FastaFileProcessing - File parsing exception (from >>> >> biojava library) >>> >> org.biojava.bio.BioException: Could not read sequence >>> >> at >>> >> >>> >>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) >>> >> at >>> >> >>> >>> org.biojavax.bio.seq.io.RichStreamReader.nextBioEntry(RichStreamReader.java:99) >>> >> at >>> >> >>> >>> edu.imperial.msc.orthologue.fasta.FastaFileProcessing.getProteinSequenceFromFASTAFile(FastaFileProcessing.java:60) >>> >> at >>> >> >>> >>> edu.imperial.msc.orthologue.core.OrthologueFinder.getFASTAEntries(OrthologueFinder.java:64) >>> >> at >>> >> >>> >>> edu.imperial.msc.orthologue.core.OrthologueFinder.<init>(OrthologueFinder.java:51) >>> >> at >>> >> >>> >>> edu.imperial.msc.orthologue.launcher.OrthologueFinderLauncher.main(OrthologueFinderLauncher.java:60) >>> >> Caused by: java.io.IOException: Mark invalid >>> >> at java.io.BufferedReader.reset(Unknown Source) >>> >> at >>> >> >>> >>> org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:202) >>> >> at >>> >> >>> >>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) >>> >> ... 5 more >>> > >>> > >>> > Interestingly if I delete the header portion of the header line (from >>> > type=protein... till the end of the line ...Dgri;) >>> > >>> >> FBpp0145468 type=protein; >>> >> >>> >>> loc=scaffold_15252:join(13219687..13219727,13219972..13220279,13220507..13220798,13220861..13221180,13221286..13221467,13222258..13222629,13226331..13226463,13226531..13226658); >>> >> ID=FBpp0145468; name=Dgri\GH11562-PA; parent=FBgn0119042,FBtr0146976; >>> >> dbxref=FlyBase:FBpp0145468,FlyBase_Annotation_IDs:GH11562-PA; >>> >> MD5=c8dc38c7197a0d3c93c78b08059e2604; length=591; release=r1.3; >>> >> species=Dgri; >>> >> >>> > >>> > It works - but I have a number of these exceptions (and I do not >>> want to >>> > edit the original data). Mind you I have longer headers in my >>> file which >>> > are parsed OK (strange!). >>> > >>> > Any ideas anyone ? Alternatively - is there a better way how to >>> get ONE >>> > SINGLE sequence from the whole fasta file give that I have the >>> accession id >>> > (FBpp0145468) ? >>> > >>> > Many Thanks >>> > JP >>> > _______________________________________________ >>> > Biojava-l mailing list - [email protected] >>> <mailto:[email protected]> >>> > http://lists.open-bio.org/mailman/listinfo/biojava-l >>> > >>> >>> -- >>> Richard Holland, BSc MBCS >>> Finance Director, Eagle Genomics Ltd >>> T: +44 (0)1223 654481 ext 3 | E: [email protected] >>> <mailto:[email protected]> >>> http://www.eaglegenomics.com/ >>> >>> >> -- >> Richard Holland, BSc MBCS >> Finance Director, Eagle Genomics Ltd >> T: +44 (0)1223 654481 ext 3 | E: [email protected] >> http://www.eaglegenomics.com/ >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: [email protected] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
