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root/owl/tags/aglappe-0.9.6/doClassifySingleModels.sh
Revision: 580
Committed: Tue Apr 8 10:01:57 2008 UTC (11 years, 7 months ago) by filippis
Original Path: trunk/doClassifySingleModels.sh
File size: 2599 byte(s)
Log Message:
createGraphDb:
-the node_id in the single_model_node table changed to AUTO_INCREMENT

doClassifySingleModels:
-the interSS for CR added

RIGraph:
-write_graph_to_db methods treat the node_id field in the single_model_node table as AUTO_INCREMENT
-write_graph_to_motiffile method added
Line File contents
1 #!/bin/sh
2 function usage {
3 echo
4 echo "Script to assign id to each possible single model type. "
5 echo
6 echo "Usage: $1 -d <db> "
7 echo "<db> the database where single model types will be stored"
8 echo
9 }
10
11 #
12 #Set default value for variables
13 #
14 db=""
15 table="single_model"
16 file="single_model.txt"
17
18 while getopts d: opt
19 do
20 case "$opt" in
21 d) db="$OPTARG";;
22 esac
23 done
24
25 if [ -z "$db" ]
26 then
27 echo "Missing arguments"
28 usage $0
29 exit 1
30 fi
31
32 arch=`uname -m`
33 case "$arch" in
34 i686)
35 mysqldir=/project/tla/dist/mysql-i686
36 ;;
37 x86_64)
38 mysqldir=/project/tla/dist/mysql
39 ;;
40 *)
41 mysqldir=/project/tla/dist/mysql-i686
42 ;;
43 esac
44
45 mysqlbin=$mysqldir/bin/mysql
46 h=white
47
48 $mysqlbin -pnieve -h $h -B -N $db <<ENDSQL
49 SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
50 SELECT 'Creating the single model table if not exists ...';
51 CREATE TABLE IF NOT EXISTS $table (
52 single_model_id INT NOT NULL AUTO_INCREMENT PRIMARY KEY,
53 dist DECIMAL(4,2) NOT NULL,
54 expBB TINYINT NOT NULL,
55 CW VARCHAR(16) NOT NULL,
56 CT VARCHAR(16) NOT NULL,
57 CR VARCHAR(80) NOT NULL,
58 d TINYINT(1) NOT NULL,
59 UNIQUE INDEX DESCRIPTION_IDX (dist, expBB, CW, CT, CR, d)
60 ) ENGINE=MyISAM;
61 ENDSQL
62
63 contactType="Ca Cb Ca/Cb Ca+Cb+Ca/Cb BB SC BB/SC BB+SC+BB/SC Ca+SC"
64
65 #(true) : no filtering
66 #((i_cid!=j_cid)OR(abs(i_num-j_num)>=2)) : remove backbone connectivity
67 #((i_cid!=j_cid)OR(abs(i_num-j_num)>=4)) : remove short range edges
68 #((i_cid!=j_cid)OR(abs(i_num-j_num)>=10)) : remove short and medium range edges
69 contactRange="(true) \
70 ((i_cid!=j_cid)OR(abs(i_num-j_num)>=2)) \
71 ((i_cid!=j_cid)OR(abs(i_num-j_num)>=4)) \
72 ((i_cid!=j_cid)OR(abs(i_num-j_num)>=10)) \
73 ((i_sstype!=j_sstype)OR(i_ssid!=j_ssid))"
74
75 echo "Outputing the models..."
76 echo -n "" > $file
77 first=`seq 2 0.5 4`
78 fours=`seq 4.1 0.1 4.9`
79 last=`seq 5 0.5 20`
80 contactDistance=`echo "$first $fours $last"`
81
82 for dist in $contactDistance
83 do
84 for ct in $contactType
85 do
86 for cr in $contactRange
87 do
88 for expBB in -1 0
89 do
90 #unweighted, undirected
91 echo -e "${dist}\t${expBB}\t1\t${ct}\t${cr}\t0" >> $file
92 #unweighted, directed
93 echo -e "${dist}\t${expBB}\t1\t${ct}\t${cr}\t1" >> $file
94 #weighted, undirected
95 echo -e "${dist}\t${expBB}\t${ct}\t${ct}\t${cr}\t0" >> $file
96 #weighted, directed
97 echo -e "${dist}\t${expBB}\t${ct}\t${ct}\t${cr}\t1" >> $file
98 done
99 done
100 done
101 done
102
103 $mysqlbin -pnieve -h $h -B -N $db <<ENDSQL
104 SELECT 'Loading the data...';
105 SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
106 LOAD DATA LOCAL INFILE "$file" IGNORE INTO TABLE $table (dist, expBB, CW, CT, CR, d);
107 ENDSQL
108
109 rm -f $file

Properties

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svn:executable *