[Biojava-l] need help

zhao guijun genome at zsu.edu.cn
Tue Feb 18 10:21:07 EST 2003


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(CharacterTokenization.java:166)
        at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.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 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 len=120|AB014087.1 Pos=16412^16413|||4475009|
AGGCCTTTCT CAAAGTGGAA GTCTCATCCT CACTTCTCTG GTTACAGTGC TGGGCCATGG 
TAACTTACAA GGCTTAGCAG GAACTGTCTG CGCACTCCCC CTTCCTGCCC ACTACCTTGT 

Best Regards,

guijun





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