FastaSequenceLoader
From BioWeka
Contents |
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Description
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Application
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Command line
To get a list of all available command line parameters for the FastaSequenceLoader class execute the class without any arguments:
java bioweka.core.converters.sequence.FastaSequenceLoader
E.g. to load a FASTA file called Test.fa with DNA sequences from the current directory and write it to an ARFF file in the same directory use the command line options -A, -i<code> and <code>-o:
java bioweka.core.converters.sequence.FastaSequenceLoader -A DNA -i Test.fa -o Test.arff
If the input file has this content:
> Test ATGC
The output file looks like:
@relation Test.fa-bioweka.core.converters.sequence.FastaSequenceLoader-D8-ADNA @attribute sequence.name string @attribute sequence.seqString string @attribute sequence.urn string @attribute sequence.length numeric @attribute sequence.alphabet string @attribute sequence.annotation.description string @attribute sequence.annotation.description_line string @data Test,atgc,urn:sequence/fasta:Test,4,DNA,?,Test
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