diff get_data/kegg_glycan/README_KEGG.md @ 0:89592faa2875 draft

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+++ b/get_data/kegg_glycan/README_KEGG.md	Wed Mar 23 14:35:56 2016 -0400
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+[TOC]
+
+# 1. findKEGG.py
+ **find entries with matching query keywords or other query data in a given database**
+
+## Works with Galaxy?
+Yes. see [findKEGG.xml](findKEGG.xml)
+
+## Command line usage
+```
+../../virtualpy/bin/activate
+python findKEGG.py
+```
+
+This will use the default settings for dbname, searchpattern and output
+To specify these :
+```
+../../virtualpy/bin/activate
+findKEGG.py -d $dbname -q $searchpattern -o $output
+```
+
+## Help
+```
+../../virtualpy/bin/activate
+python findKEGG.py -h
+```
+
+## Unit Testing?
+Yes. Use test_findKEGG.py
+
+```
+../../virtualpy/bin/activate
+python  test_findKEGG.py
+```
+
+# 2. getkcfKEGG,py
+ **get – retrieves given database entries _but only for GLYCANS_**
+
+
+## Works with Galaxy?
+Yes. see [getkcfKEGG.xml](getkcfKEGG.xml)
+
+## Command line usage
+
+```
+../../virtualpy/bin/activate
+cat "G00092" > input
+python getkcfKEGG.py
+```
+
+This will use the default settings for input, kcfout and dbout
+To specify these :
+```
+../../virtualpy/bin/activate
+    getkcfKEGG.py -i $input -k $kcfout -d $dbout
+```
+
+## Help
+```
+../../virtualpy/bin/activate
+python getkcfKEGG.py -h
+```
+
+## Unit Testing?
+Yes. Use test_getkcfKEGG.py
+
+```
+../../virtualpy/bin/activate
+python  test_getkcfKEGG.py
+```
+
+# 3. linkKEGG.py
+ **link – find related entries by using database cross-references**
+
+## Works with Galaxy?
+Yes. see [linkKEGG.xml](linkKEGG.xml)
+
+## Command line usage
+```
+../../virtualpy/bin/activate
+python linkKEGG.py
+```
+
+This will use the default settings for targetdb, source and output
+linkKEGG.py -t $targetdb -s $source -o $output
+To specify these :
+```
+../../virtualpy/bin/activate
+linkKEGG.py -t $targetdb -s $source -o $output
+```
+
+## Help
+```
+../../virtualpy/bin/activate
+python linkKEGG.py -h
+```
+
+## Unit Testing?
+Yes. Use test_linkKEGG.py
+
+```
+../../virtualpy/bin/activate
+python  test_linkKEGG.py
+```
+