Mercurial > repos > test-svm > kmersvm_test
changeset 2:e8dcc2ed0f9f draft
Included bugfix, README
| author | test-svm |
|---|---|
| date | Sun, 05 Aug 2012 16:32:03 -0400 |
| parents | a8cbea0008d4 |
| children | 5b3d8ca0bf20 |
| files | kmersvm/README.txt kmersvm/scripts/.nullseq_build_indices.py.swp kmersvm/scripts/make_profile.py kmersvm/scripts/split_genome.py kmersvm/svm_enh/split_genome.pyc |
| diffstat | 5 files changed, 46 insertions(+), 3 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kmersvm/README.txt Sun Aug 05 16:32:03 2012 -0400 @@ -0,0 +1,45 @@ +DEPENDENCIES: +************* +KmerSVM requires the following software: + + *Shogun Toolbox, v0.9.3 - v1.10 + *Swig + *Numpy + *Bitarray + *R + *ROCR R Package + +Further, KmerSVM has been tested on Python 2.6, 2.7. + +REQUIRED FILES: +*************** +For efficient access to genome-wide data "Generate Null Sequence" and +"Sequence Profiles" rely on access to binary files (indices) generated +by using the script 'nullseq_build_indices.py'. Download the *.tar or +*.zip files for each genome to be analyzed. To create indices for a +specific genome, call nullseq_build_indices.py as follows: + +python nullseq_build_indices.py <GENOME ARCHIVE FILE> <GENOME BUILD> + +Next create a nullseq_indices.loc file according to the instructions +in nullseq_indices.loc.sample, providing the path to the created indices. + +To generate FASTA files for training or scoring purposes, KmerSVM uses +the built-in tool "Fetch Sequences", which looks for genomes in *.nib or +*.2bit format. Download genomes related to your data and update the +'alignseq.loc' file to include the location of these genomes according +to directions in that file. + +TOOL_CONF.XML: +************** +Add the following lines to tool_conf.xml: + + <section name="SVM Tools" id="kmersvm"> + <tool file="kmersvm/classify.xml"/> + <tool file="kmersvm/nullseq.xml"/> + <tool file="kmersvm/rocprcurve.xml"/> + <tool file="kmersvm/train.xml"/> + <tool file="kmersvm/split_genome.xml"/> + <tool file="kmersvm/seqprofile.xml" /> + </section> +
--- a/kmersvm/scripts/make_profile.py Sun Aug 05 15:39:52 2012 -0400 +++ b/kmersvm/scripts/make_profile.py Sun Aug 05 16:32:03 2012 -0400 @@ -73,8 +73,7 @@ def main(): parser = optparse.OptionParser() - - if len(sys.argv) != 4: + if len(sys.argv) != 5: print "Usage:", sys.argv[0], "BEDFILE BUILDNAME BASE_DIR OUT_FILE" sys.exit() parser.add_option("-o", dest="output", default="seq_profile.txt")