Mercurial > repos > test-svm > kmersvm_test

changeset 3:5b3d8ca0bf20 draft

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Uploaded updated README
author test-svm
date Sun, 05 Aug 2012 16:47:06 -0400
parents e8dcc2ed0f9f
children f2130156fd5d
files kmersvm/README.txt kmersvm/nullseq.xml kmersvm/nullseq_output.bed kmersvm/nullseq_test.bed kmersvm/scripts/.nullseq_build_indices.py.swp kmersvm/split_genome.loc
diffstat 6 files changed, 19 insertions(+), 218 deletions(-) [+]
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--- a/kmersvm/README.txt	Sun Aug 05 16:32:03 2012 -0400
+++ b/kmersvm/README.txt	Sun Aug 05 16:47:06 2012 -0400
@@ -21,8 +21,9 @@
 
 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. 
+Next copy nullseq_indices.loc.sample to tool-data/nullseq_indices.loc 
+and add the path to the created indices following the instructions 
+included in that file.
 
 To generate FASTA files for training or scoring purposes, KmerSVM uses
 the built-in tool "Fetch Sequences", which looks for genomes in *.nib or
@@ -30,6 +31,8 @@
 'alignseq.loc' file to include the location of these genomes according
 to directions in that file.
 
+Move the file sample_roc_chen.png to the 'tool-data' file.
+
 TOOL_CONF.XML:
 **************
 Add the following lines to tool_conf.xml:
@@ -43,3 +46,17 @@
     <tool file="kmersvm/seqprofile.xml" />
   </section>
 
+Tool Tests:
+***********
+To run tests on the tools "Train SVM", "Score Sequences of Interest" and
+"Split Genome", move the following files to the 'test-data' directory:
+
+  *classify_output.out
+  *classify_test.fa
+  *kmersvm_output_weights.out
+  *test_positive.fa
+  *test_negative.fa
+  *test_weights.out
+  *train_predictions.out
+
+IDs for KmerSVM tests can be found by calling run_functional_tests.sh with the '-list' flag.
--- a/kmersvm/nullseq.xml	Sun Aug 05 16:32:03 2012 -0400
+++ b/kmersvm/nullseq.xml	Sun Aug 05 16:47:06 2012 -0400
@@ -28,17 +28,6 @@
   <outputs>
     <data format="interval" name="nullseq_output" from_work_dir="nullseq_output.bed" />
   </outputs>
-   <tests>
-    <test>
-      <param name="input" value="nullseq_test.bed" ftype="bed" />
-      <param name="fold" value="1" />
-      <param name="gc_err" value="0.02" />
-      <param name="rpt_err" value="0'02" />
-      <param name="rseed" value="1" />
-      <param name="indices_path"  value="hg19" />
-      <output name="output" file="nullseq_output.bed" />
-    </test> 
-  </tests>
   <help>
   
 **What it does**
--- a/kmersvm/nullseq_output.bed	Sun Aug 05 16:32:03 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
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--- a/kmersvm/nullseq_test.bed	Sun Aug 05 16:32:03 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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\ No newline at end of file
Binary file kmersvm/scripts/.nullseq_build_indices.py.swp has changed
--- a/kmersvm/split_genome.loc	Sun Aug 05 16:32:03 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-mm9	Mouse(mm9)	/Users/kipperfletez-brant/galaxy-dist/tools/kmersvm/mm9nib
-mm8	Mouse(mm8)	/Users/kipperfletez-brant/galaxy-dist/tools/kmersvm/mm8nib
-hg18	Human(hg18)	/Users/kipperfletez-brant/galaxy-dist/tools/kmersvm/hg18nib
-hg19	Human(hg19)	/Users/kipperfletez-brant/galaxy-dist/tools/kmersvm/hg19nib
-hg192bit	Human(hg192bit)	/Users/kipperfletez-brant/galaxy-dist/tools/kmersvm/hg19.2bit
\ No newline at end of file