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 (14 years, 1 month 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	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