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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