Mercurial > repos > chrisb > gap_all_glycan_tools

diff manipulate/extend_linearcode/README_extend.md @ 0:89592faa2875 draft
Uploaded
author: chrisb
date: Wed, 23 Mar 2016 14:35:56 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/manipulate/extend_linearcode/README_extend.md	Wed Mar 23 14:35:56 2016 -0400
@@ -0,0 +1,55 @@
+[TOC]
+
+# lc_extend.py
+This tool provides all permutations of linear code with uncertain leaves.
+
+*Buggy, not guaranteed to function properly...*
+
+## Works with Galaxy?
+Yes. see [lc_extend.xml](lc_extend.xml)
+
+## Command line usage
+
+```
+../../virtualpy/bin/activate
+python lc_extend.py -i $input -o $output -l $logfile $appendorextend
+```
+
+## Example input / output
+Query sequence
+
+```
+(Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN,M)
+(A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)
+```
+
+Default Output sequence
+
+```
+((M??)X??)(Ma2Ma3(Ma3)(Ma6)Ma6)Mb4GNb4GN
+(A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)
+```
+
+Extended Output sequence _(not recommended)_
+
+```
+M??Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN
+Ma2Ma3(M??Ma3(Ma6)Ma6)Mb4GNb4GN
+Ma2Ma3(Ma3(M??Ma6)Ma6)Mb4GNb4GN
+(A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)
+```
+
+## Help
+```
+../../virtualpy/bin/activate
+python lc_extend.py -h
+```
+
+## Unit Testing?
+Yes.
+
+
+```
+../../virtualpy/bin/activate
+python  test_lc_extend.py
+```