Sleipnir
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Txt2Bin converts between SVM Light compatible text feature files, Sleipnir binary feature files containing the same information (Sleipnir::CSVM::Learn and Sleipnir::CSVM::Evaluate), and DAT/DAB files containing data. This is primarily useful for condensing multiple DAT/DAB files into a binary SVM example file for learning/evaluation or for displaying the contents of such a file as human-readable text.
Txt2Bin -f dat -t bin -w <answers.dab> -o <examples.bin> <data.dab>*
Generates the binary SVM examples/features file examples.bin
using the labels for gene pairs in answers.dab
and the data (features) for those gene pairs in the one or more data.dab
files.
Txt2Bin -f txt -t bin -i <examples.txt> -o <examples.bin>
Convert the SVM Light text-based examples file examples.txt
into a Sleipnir binary SVM examples file examples.bin
.
Txt2Bin -f bin -t txt -i <examples.bin> -o <examples.txt>
Convert the Sleipnir binary SVM examples file examples.bin
into an SVM Light text-based examples file examples.txt
.
package "Txt2Bin"
version "1.0"
purpose "SVM binary input manipulator"
section "Main"
option "input" i "Input text/binary file"
string typestr="filename"
option "answers" w "Answer file"
string typestr="filename"
option "output" o "Output binary file"
string typestr="filename"
section "Miscellaneous"
option "from" f "Source format"
values="txt","dat","bin" default="txt"
option "to" t "Target format"
values="txt","bin" default="bin"
option "matrix" m "Read/write simple matrix format"
flag off
section "Learning/Evaluation"
option "genes" g "Gene inclusion file"
string typestr="filename"
option "genex" G "Gene exclusion file"
string typestr="filename"
section "Optional"
option "verbosity" v "Message verbosity"
int default="5"
Flag | Default | Type | Description |
---|---|---|---|
None | None | DAT/DAB files | When converting from DAT/DAB files to SVM features, the data files to be read. Each gene pair becomes one example in the output and each DAT/DAB one feature. |
-i | None | Text or binary feature file | When converting from text or binary feature files, the feature file to be opened. Can be in SVM Light text format or Sleipnir binary format. |
-w | None | stdin | When converting from DAT/DAB data files, the gold standard answer file used to label the resulting training examples. |
-f | txt | txt, dat, or bin | Format of input file to be converted from. |
-t | bin | txt or bin | Format of output file to be converted to. |
-g | None | Text gene list | If given, use only gene pairs for which both genes are in the list. For details, see Sleipnir::CDat::FilterGenes. |
-G | None | Text gene list | If given, use only gene pairs for which neither gene is in the list. For details, see Sleipnir::CDat::FilterGenes. |