This is a guess more than anything else (but probably a good one): I don't this that the fasta reader accepts spaces in the sequence.
This explains the error message, that it doesn't contain the character ' '. I don't remember the specifications for the fasta format, but I don't think it includes having spaces in the sequence. Fran?ois -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] On Behalf Of zhao guijun Sent: 17 f¨¦vrier, 2003 21:00 To: [EMAIL PROTECTED] Subject: [Biojava-l] need help hello, could anyone tell me why I got such errors? /usr/java2/bin/java ReadFasta imsIND020717.fas DNA org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't contain character: at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTok enization.java:166) at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(C haracterTokenization.java:237) at org.biojava.bio.seq.io.FastaFormat.readSequenceData(FastaFormat.java:150 ) at org.biojava.bio.seq.io.FastaFormat.readSequence(FastaFormat.java:114) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:100) rethrown as org.biojava.bio.BioException: Could not read sequence at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:103) at org.biojava.bio.seq.io.SeqIOTools.readFasta(SeqIOTools.java:244) at ReadFasta.main(ReadFasta.java:17) the reading file(imsIND020717.fas) format is like the following: >gnl|IMS-JST_InsDel_IND|IMS-JST075587_Major allelePos=61 total >gnl|len=121|AB014087.1 Pos=16412^16413|||4475009| AGGCCTTTCT CAAAGTGGAA GTCTCATCCT CACTTCTCTG GTTACAGTGC TGGGCCATGG G TAACTTACAA GGCTTAGCAG GAACTGTCTG CGCACTCCCC CTTCCTGCCC ACTACCTTGT >gnl|IMS-JST_InsDel_IND|IMS-JST075587_Minor allelePos=60^61 total >gnl|len=120|AB014087.1 Pos=16412^16413|||4475009| AGGCCTTTCT CAAAGTGGAA GTCTCATCCT CACTTCTCTG GTTACAGTGC TGGGCCATGG TAACTTACAA GGCTTAGCAG GAACTGTCTG CGCACTCCCC CTTCCTGCCC ACTACCTTGT Best Regards, guijun _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
