Dot to XDSL

Dot to XDSL

Postby vlee14 » Mon Dec 01, 2014 1:33 pm

MODULE NAME
dot-to-xdsl - compiled and built with the makefile in the directory

AVAILABILITY
Git repository (public)

DESCRIPTION
This module converts a dot file to an XDSL file.

EXAMPLES

If you copy and paste the following contents of a dot file into InputFile.dot:

digraph abstract
{
0 [label="PAH"];
1 [label="NRCAM"];
2 [label="MAP2"];
3 [label="RUNX1T1"];
4 [label="ENO2"];
5 [label="CRISP1"];
6 [label="NR4A3"];
7 [label="RLN2"];
8 [label="LDHA"];
9 [label="GSTM3"];
10 [label="LAMC2"];
11 [label="COL6A1"];
12 [label="SLC11A2"];
13 [label="NTRK3"];
14 [label="PGK1"];
15 [label="FGA"];
16 [label="STAT5B"];
17 [label="TMEM41B"];
18 [label="PIGC"];
19 [label="PEX5"];
20 [label="UGP2"];
21 [label="RUNX1"];
22 [label="PIGK"];
23 [label="MTM1"];
24 [label="ADRA2A"];
25 [label="NRAS"];
26 [label="BCR"];
27 [label="MAP7"];
28 [label="MAPK6"];
29 [label="NEDD4"];
30 [label="TXK"];
31 [label="ETV3"];
32 [label="KPNA4"];
33 [label="DDX18"];
34 [label="RAD50"];
35 [label="DDX10"];
36 [label="BCLAF1"];
37 [label="FEZ1"];
38 [label="LAMP1"];
39 [label="GCLM"];
40 [label="JAK1"];
41 [label="OTUD4"];
42 [label="FXR1"];
43 [label="TMED10"];
44 [label="HLA-G"];
45 [label="APP"];
46 [label="NRIP1"];
47 [label="ESR2"];
48 [label="SEC23A"];
49 [label="PPP1CC"];
50 [label="MYCN"];
51 [label="TMED2"];
52 [label="ATF2"];
53 [label="TMF1"];
54 [label="CA6"];
55 [label="GOLGA4"];
56 [label="HSP90AB1"];
57 [label="CASP8"];
58 [label="ATP5F1"];
59 [label="SCN1B"];
60 [label="CYCS"];
61 [label="CD34"];
62 [label="ABCE1"];
63 [label="AZGP1"];
64 [label="RPS5"];
65 [label="KRT18"];
66 [label="PEA15"];
67 [label="AES"];
68 [label="ACSM3"];
69 [label="RQCD1"];
70 [label="CTSE"];
71 [label="EIF4A1"];
72 [label="HSPA5"];
73 [label="CD40"];
74 [label="ANKS1A"];
75 [label="FLNC"];
76 [label="PROL1"];
77 [label="HAAO"];
78 [label="DNM1"];
79 [label="HOXA1"];
80 [label="PPP1R10"];
81 [label="PF4V1"];
82 [label="SDS"];
83 [label="NUMB"];
84 [label="SERPINB6"];
85 [label="COL17A1"];
86 [label="POLR2A"];
87 [label="IFIT2"];
88 [label="KRT1"];
89 [label="PTGS1"];
90 [label="TBR1"];
91 [label="DECR1"];
92 [label="MC2R"];
93 [label="GLUL"];
94 [label="KCNJ8"];
95 [label="S100A5"];
96 [label="MT2A"];
97 [label="ARSE"];
98 [label="FKBP8"];
99 [label="GPKOW"];
100 [label="TNFRSF9"];
101 [label="CX3CL1"];
102 [label="GABRA1"];
103 [label="STARD8"];
104 [label="SLC19A1"];
105 [label="FABP4"];
106 [label="GYPB"];
107 [label="ANKRD1"];
108 [label="AAMP"];
109 [label="SULT1C2"];
110 [label="GUCA2B"];
111 [label="GRIN2C"];
112 [label="GMPR"];
113 [label="SEPHS2"];
114 [label="CCL21"];
115 [label="PTMS"];
116 [label="LMNB1"];
117 [label="CLTCL1"];
118 [label="TRPV6"];
119 [label="SLC18A3"];
120 [label="MYL9"];
121 [label="TNNI3"];
122 [label="CDX2"];
123 [label="PLA2G5"];
124 [label="IFNA16"];
125 [label="ST6GALNAC2"];
126 [label="FES"];
127 [label="CDA"];
128 [label="SELPLG"];
129 [label="PDE2A"];
130 [label="IFI27"];
131 [label="SLC8A1"];
132 [label="SCN5A"];
133 [label="ZP2"];
134 [label="GATA1"];
135 [label="NRGN"];
136 [label="GIP"];
137 [label="PSG1"];
138 [label="TLE1"];
139 [label="GP1BA"];
140 [label="PRM2"];
141 [label="EPHB1"];
142 [label="LGALS3"];
143 [label="CD72"];
144 [label="KCNJ3"];
145 [label="SLC5A1"];
146 [label="HTR1D"];
147 [label="MMP9"];
148 [label="HSD3B2"];
149 [label="CYP1B1"];
150 [label="IFIT3"];
151 [label="IQGAP2"];
152 [label="ACOX2"];
153 [label="BATF"];
154 [label="KLRD1"];
155 [label="CDX1"];
156 [label="SFTPC"];
157 [label="C6orf10"];
158 [label="LPL"];
159 [label="CLEC3B"];
160 [label="SECTM1"];
161 [label="XCL1"];
162 [label="IL13RA2"];
163 [label="TMOD1"];
164 [label="IGFBP2"];
165 [label="NOTCH3"];

52->0;
25->1;
50->2;
33->3;
64->4;
66->5;
55->6;
28->7;
25->8;
33->9;
28->10;
66->11;
4->12;
52->13;
8->14;
25->14;
41->15;
38->16;
49->17;
46->18;
62->19;
43->20;
8->21;
46->22;
28->23;
8->24;
28->25;
49->26;
62->27;
62->28;
23->29;
55->30;
70->31;
28->32;
46->33;
28->34;
58->34;
28->35;
32->36;
27->37;
66->38;
34->39;
71->40;
25->41;
46->42;
18->43;
58->44;
8->45;
108->46;
28->47;
46->48;
27->49;
60->50;
46->51;
32->52;
62->53;
46->54;
60->55;
46->56;
41->57;
33->58;
57->59;
25->60;
24->61;
46->62;
8->63;
8->64;
8->65;
19->66;
62->67;
64->68;
60->69;
68->70;
25->71;
28->72;
77->73;
83->74;
11->75;
98->77;
11->78;
72->79;
86->81;
126->82;
99->83;
99->84;
139->85;
98->86;
83->87;
106->88;
66->89;
74->91;
98->92;
47->93;
83->94;
98->95;
19->96;
112->97;
99->98;
80->99;
108->100;
66->101;
133->102;
74->103;
160->104;
33->105;
90->106;
76->107;
99->108;
111->109;
99->110;
140->111;
98->112;
91->113;
136->114;
56->115;
83->116;
91->117;
47->118;
95->119;
98->120;
76->121;
92->122;
136->123;
54->124;
108->125;
160->126;
66->127;
104->128;
66->129;
67->130;
66->131;
137->132;
74->133;
112->135;
79->136;
76->137;
98->138;
46->139;
113->139;
77->140;
95->141;
35->142;
68->150;
149->153;
159->154;
124->155;
122->156;
90->157;
62->158;
104->159;
139->160;
133->161;
75->162;
30->164;

labeljust="l";
label = "Banjo Version 2.2.0\nHigh scoring network, score: -21149.1338\nProject: THI-TS\nUser: cwyoo\nDataset: 19var-505cases";
}

You will get the following results:

<?xml version="1.0" encoding="ISO-8859-1"?>
<smile version="1.0" id="Unnamed" numsamples="1000" discsamples="10000">
<nodes>
<cpt id="PPP1R10">
<state id="State0" />
<state id="State1" />
<probabilities>0.5 0.5</probabilities>
</cpt>
<cpt id="GPKOW">
<state id="State0" />
<state id="State1" />
<parents>PPP1R10</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="AAMP">
<state id="State0" />
<state id="State1" />
<parents>GPKOW</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="NRIP1">
<state id="State0" />
<state id="State1" />
<parents>AAMP</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="ABCE1">
<state id="State0" />
<state id="State1" />
<parents>NRIP1</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="MAPK6">
<state id="State0" />
<state id="State1" />
<parents>ABCE1</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="KPNA4">
<state id="State0" />
<state id="State1" />
<parents>MAPK6</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="ATF2">
<state id="State0" />
<state id="State1" />
<parents>KPNA4</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="PAH">
<state id="State0" />
<state id="State1" />
<parents>ATF2</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="NRAS">
<state id="State0" />
<state id="State1" />
<parents>MAPK6</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="NRCAM">
<state id="State0" />
<state id="State1" />
<parents>NRAS</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="LAMC2">
<state id="State0" />
<state id="State1" />
<parents>MAPK6</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="TNFRSF9">
<state id="State0" />
<state id="State1" />
<parents>AAMP</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="PEX5">
<state id="State0" />
<state id="State1" />
<parents>ABCE1</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="PEA15">
<state id="State0" />
<state id="State1" />
<parents>PEX5</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="CX3CL1">
<state id="State0" />
<state id="State1" />
<parents>PEA15</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
</cpt>
<cpt id="NUMB">
<state id="State0" />
<state id="State1" />
<parents>GPKOW</parents>
<probabilities>0.5 0.5 0.5 0.5</probabilities>
.
.
.
</node>
<node id="NEDD4">
<name>NEDD4</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>696 516 772 552</position>
</node>
<node id="RUNX1T1">
<name>RUNX1T1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>500 608 576 644</position>
</node>
<node id="TXK">
<name>TXK</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>892 286 968 322</position>
</node>
<node id="ETV3">
<name>ETV3</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>1088 10 1164 46</position>
</node>
<node id="KPNA4">
<name>KPNA4</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>598 378 674 414</position>
</node>
<node id="DDX18">
<name>DDX18</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>402 424 478 460</position>
</node>
<node id="RAD50">
<name>RAD50</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>598 424 674 460</position>
</node>
<node id="DDX10">
<name>DDX10</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>598 470 674 506</position>
</node>
<node id="BCLAF1">
<name>BCLAF1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>696 562 772 598</position>
</node>
<node id="FEZ1">
<name>FEZ1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>598 516 674 552</position>
</node>
<node id="LAMP1">
<name>LAMP1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>696 608 772 644</position>
</node>
<node id="GCLM">
<name>GCLM</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>696 654 772 690</position>
</node>
<node id="ENO2">
<name>ENO2</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>892 332 968 368</position>
</node>
<node id="JAK1">
<name>JAK1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>794 470 870 506</position>
</node>
<node id="OTUD4">
<name>OTUD4</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>696 700 772 736</position>
</node>
<node id="FXR1">
<name>FXR1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>402 470 478 506</position>
</node>
<node id="TMED10">
<name>TMED10</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>500 654 576 690</position>
</node>
<node id="HLA_G">
<name>HLA_G</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>598 562 674 598</position>
</node>
<node id="APP">
<name>APP</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>794 516 870 552</position>
</node>
<node id="NRIP1">
<name>NRIP1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>304 286 380 322</position>
</node>
<node id="ESR2">
<name>ESR2</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>598 608 674 644</position>
</node>
<node id="SEC23A">
<name>SEC23A</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>402 516 478 552</position>
</node>
<node id="PPP1CC">
<name>PPP1CC</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>598 654 674 690</position>
</node>
<node id="CRISP1">
<name>CRISP1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>696 746 772 782</position>
</node>
<node id="MYCN">
<name>MYCN</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>794 562 870 598</position>
</node>
<node id="TMED2">
<name>TMED2</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>402 562 478 598</position>
</node>
<node id="ATF2">
<name>ATF2</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>696 792 772 828</position>
</node>
<node id="TMF1">
<name>TMF1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>500 700 576 736</position>
</node>
<node id="CA6">
<name>CA6</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>402 608 478 644</position>
</node>
<node id="GOLGA4">
<name>GOLGA4</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>794 608 870 644</position>
</node>
<node id="HSP90AB1">
<name>HSP90AB1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>402 654 478 690</position>
</node>
<node id="CASP8">
<name>CASP8</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>794 654 870 690</position>
</node>
<node id="ATP5F1">
<name>ATP5F1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>500 746 576 782</position>
</node>
<node id="SCN1B">
<name>SCN1B</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>892 378 968 414</position>
</node>
<node id="NR4A3">
<name>NR4A3</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>892 424 968 460</position>
</node>
<node id="CYCS">
<name>CYCS</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>696 838 772 874</position>
</node>
<node id="CD34">
<name>CD34</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>892 470 968 506</position>
</node>
<node id="ABCE1">
<name>ABCE1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>402 700 478 736</position>
</node>
<node id="AZGP1">
<name>AZGP1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>794 700 870 736</position>
</node>
<node id="RPS5">
<name>RPS5</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>794 746 870 782</position>
</node>
<node id="KRT18">
<name>KRT18</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>794 792 870 828</position>
</node>
<node id="PEA15">
<name>PEA15</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>598 700 674 736</position>
</node>
<node id="AES">
<name>AES</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>500 792 576 828</position>
</node>
<node id="ACSM3">
<name>ACSM3</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>892 516 968 552</position>
</node>
<node id="RQCD1">
<name>RQCD1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>794 838 870 874</position>
</node>
<node id="RLN2">
<name>RLN2</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>598 746 674 782</position>
</node>
<node id="CTSE">
<name>CTSE</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>990 194 1066 230</position>
</node>
<node id="EIF4A1">
<name>EIF4A1</name>
<interior color="e5f6f7" />
<outline color="0000bb" />
<font color="000000" name="MS Sans Serif" size="8" />
<position>696 884 772 920</position>
</node>
<node id="HSPA5">
<name>HSPA5</name>
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</smile>

..outputted in the file output.xdsl.

FILES
Output.XDSL; an XDSL file containing the bayesian network of the dot file that is inputted into the module that can read by the program Genie. The file should be in the same directory.
vlee14
 
Posts: 38
Joined: Wed Sep 24, 2014 4:53 pm

Re: Dot to XDSL

Postby cwyoo » Thu Dec 04, 2014 1:39 pm

Where do you specify the dataset name, if you want to include the dataset?
cwyoo
Site Admin
 
Posts: 377
Joined: Sun Jun 22, 2014 2:38 pm

Re: Dot to XDSL

Postby cwyoo » Mon Nov 28, 2016 4:02 pm

cwyoo wrote:Where do you specify the dataset name, if you want to include the dataset?


The code version that was submitted to Git (public domain, "Dot to XDSL") on Nov 21, 2016, assumes dataset is stored in Dataset.txt (tab separated) and dot file is stored in InputFile.dot. Resulted xdsl file will be stored in output.xdsl.
cwyoo
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