owl/trunk/doClassifySingleModels.sh

#!/bin/sh
function usage {
        echo
        echo "Script to assign id to each possible single model type. "
        echo
        echo "Usage: $1 -d <db> "
        echo "<db>      the database where single model types will be stored"
        echo
} 

#
#Set default value for variables
#
db=""
table="single_model"
file="single_model.txt"

while getopts d: opt
do
  case "$opt" in
        d) db="$OPTARG";;       
  esac
done

if [ -z "$db" ]
then
        echo "Missing arguments"
        usage $0
        exit 1
fi

arch=`uname -m`
case "$arch" in
    i686)
        mysqldir=/project/tla/dist/mysql-i686
    ;;
    x86_64)
        mysqldir=/project/tla/dist/mysql
    ;;
    *)
        mysqldir=/project/tla/dist/mysql-i686
    ;;
esac

mysqlbin=$mysqldir/bin/mysql
h=white

$mysqlbin -pnieve -h $h -B -N $db <<ENDSQL
SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
SELECT 'Creating the single model table if not exists ...';
CREATE TABLE IF NOT EXISTS $table (
        single_model_id INT NOT NULL AUTO_INCREMENT PRIMARY KEY,
        dist DECIMAL(4,2) NOT NULL,
        expBB TINYINT NOT NULL,
        CW VARCHAR(16) NOT NULL,
        CT VARCHAR(16) NOT NULL,
        CR VARCHAR(80) NOT NULL,
        d TINYINT(1) NOT NULL,
        UNIQUE INDEX DESCRIPTION_IDX (dist, expBB, CW, CT, CR, d)
) ENGINE=MyISAM;
ENDSQL

contactType="Ca Cb Ca/Cb Ca+Cb+Ca/Cb BB SC BB/SC BB+SC+BB/SC Ca+SC"

#(true)                                                                         : no filtering
#((i_cid!=j_cid)OR(abs(i_num-j_num)>=2))        : remove backbone connectivity 
#((i_cid!=j_cid)OR(abs(i_num-j_num)>=4))        : remove short range edges
#((i_cid!=j_cid)OR(abs(i_num-j_num)>=10))       : remove short and medium range edges
contactRange="(true) \
                        ((i_cid!=j_cid)OR(abs(i_num-j_num)>=2)) \
                        ((i_cid!=j_cid)OR(abs(i_num-j_num)>=4)) \
                        ((i_cid!=j_cid)OR(abs(i_num-j_num)>=10)) \
                        ((i_sstype!=j_sstype)OR(i_ssid!=j_ssid))"

echo "Outputing the models..."
echo -n "" > $file
first=`seq 2 0.5 4`
fours=`seq 4.1 0.1 4.9`
last=`seq 5 0.5 20`
contactDistance=`echo "$first $fours $last"`

for dist in $contactDistance
do
        for ct in $contactType
        do
                for cr in $contactRange
                do                              
                        for expBB in -1 0
                        do
                                #unweighted, undirected
                                echo -e "${dist}\t${expBB}\t1\t${ct}\t${cr}\t0" >> $file
                                #unweighted, directed
                                echo -e "${dist}\t${expBB}\t1\t${ct}\t${cr}\t1" >> $file
                                #weighted, undirected
                                echo -e "${dist}\t${expBB}\t${ct}\t${ct}\t${cr}\t0" >> $file
                                #weighted, directed
                                echo -e "${dist}\t${expBB}\t${ct}\t${ct}\t${cr}\t1" >> $file
                        done
                done
        done
done

$mysqlbin -pnieve -h $h -B -N $db <<ENDSQL
SELECT 'Loading the data...';
SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
LOAD DATA LOCAL INFILE "$file" IGNORE INTO TABLE $table (dist, expBB, CW, CT, CR, d);
ENDSQL

rm -f $file
Revision:	580
Committed:	Tue Apr 8 10:01:57 2008 UTC (12 years, 5 months ago) by filippis
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	User	Rev	File contents
1	filippis	576	#!/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	filippis	580	((i_cid!=j_cid)OR(abs(i_num-j_num)>=10)) \
73			((i_sstype!=j_sstype)OR(i_ssid!=j_ssid))"
74	filippis	576
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