Liu11 code input format
TextWrangler replace ',' in pairs.csv to white space, save as 'pair.txt'.
applejack:run.ppi hqin$ Parse pairs.txt
pairs.txt
# N= 4478, E= 13667
In total it takes 0.20 s
applejack:run.ppi hqin$ head pairs.txt.nodemap
0 YMR047C
1 YGR218W
2 YOR128C
3 YCR067C
4 YLL028W
5 YHR188C
6 YMR292W
7 YDR414C
8 YNL078W
9 YHR187W
applejack:run.ppi hqin$ ControllabilityAnalysis pairs.txt > _typscript.txt
_typescript.txt
Read Standard Elist:
N= 4478
E= 13667
<k> = 6.10406
Number of driver nodes: Nd= 2295
Control profile (Ns, Ne, Ni)=(1321,0,974)
Nd= 2295
Type-I node classification: (Ncn, Nrn, Non)=(460,1961,2057)
Type-II node classification: (Ncn, Nrn, Non)=(1321,1526,1631)
Link classification: (Ncl, Nrl, Nol)=(796,6079,6792)
Clustering Coefficient: <LCC>= 0.0806148; GCC=0.0604306; <LCC>_d=0.0403074; GCC_d=0.0302153
0 72348.1
1 53025.5
2 5971.48
3 10
4 3242.97
5 705.874
6 0
7 7391.21
8 2264.2
... ...
... ...
<Betweeness Centrality> = 1085.74<Closeness Centrality> = 1085.74
<Hub Centrality> = 0.00255414
<Authority Centrality> = 0.00232173
In total it takes 4.87 s.
applejack:run.ppi hqin$ ll
total 1328
-rw-r--r-- 1 hqin staff 42K Feb 15 06:51 _typscript.txt
lrwxr-xr-x 1 hqin staff 17B Feb 15 06:48 pairs.txt -> ../data/pairs.txt
-rw-r--r-- 1 hqin staff 107K Feb 15 06:49 pairs.txt.elist.b
-rw-r--r-- 1 hqin staff 117K Feb 15 06:49 pairs.txt.elist.t
-rw-r--r-- 1 hqin staff 240K Feb 15 06:51 pairs.txt.linktype
-rw-r--r-- 1 hqin staff 56K Feb 15 06:49 pairs.txt.nodemap
-rw-r--r-- 1 hqin staff 80K Feb 15 06:51 pairs.txt.nodetype
-rw-r--r-- 1 hqin staff 213B Feb 15 06:51 pairs.txt.output
applejack:run.ppi hqin$ wc -l pairs.txt.linktype
13668 pairs.txt.linktype
applejack:run.ppi hqin$ head pairs.txt.linktype
#source target LinkType
YMR047C YGR218W 1
YOR128C YCR067C 2
YLL028W YHR188C 1
Q: Liu11 treat PPI as directed graph. How did PNAS16 paper deal with this problem?
Reference
Liu 2011 Nature.
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