|
0
|
1 [TOC]
|
|
|
2
|
|
|
3 # lc_extend.py
|
|
|
4 This tool provides all permutations of linear code with uncertain leaves.
|
|
|
5
|
|
|
6 *Buggy, not guaranteed to function properly...*
|
|
|
7
|
|
|
8 ## Works with Galaxy?
|
|
|
9 Yes. see [lc_extend.xml](lc_extend.xml)
|
|
|
10
|
|
|
11 ## Command line usage
|
|
|
12
|
|
|
13 ```
|
|
|
14 ../../virtualpy/bin/activate
|
|
|
15 python lc_extend.py -i $input -o $output -l $logfile $appendorextend
|
|
|
16 ```
|
|
|
17
|
|
|
18 ## Example input / output
|
|
|
19 Query sequence
|
|
|
20
|
|
|
21 ```
|
|
|
22 (Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN,M)
|
|
|
23 (A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)
|
|
|
24 ```
|
|
|
25
|
|
|
26 Default Output sequence
|
|
|
27
|
|
|
28 ```
|
|
|
29 ((M??)X??)(Ma2Ma3(Ma3)(Ma6)Ma6)Mb4GNb4GN
|
|
|
30 (A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)
|
|
|
31 ```
|
|
|
32
|
|
|
33 Extended Output sequence _(not recommended)_
|
|
|
34
|
|
|
35 ```
|
|
|
36 M??Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN
|
|
|
37 Ma2Ma3(M??Ma3(Ma6)Ma6)Mb4GNb4GN
|
|
|
38 Ma2Ma3(Ma3(M??Ma6)Ma6)Mb4GNb4GN
|
|
|
39 (A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)
|
|
|
40 ```
|
|
|
41
|
|
|
42 ## Help
|
|
|
43 ```
|
|
|
44 ../../virtualpy/bin/activate
|
|
|
45 python lc_extend.py -h
|
|
|
46 ```
|
|
|
47
|
|
|
48 ## Unit Testing?
|
|
|
49 Yes.
|
|
|
50
|
|
|
51
|
|
|
52 ```
|
|
|
53 ../../virtualpy/bin/activate
|
|
|
54 python test_lc_extend.py
|
|
|
55 ```
|
