ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/owl/tags/aglappe-0.9.3/createGraphDb.sh
Revision: 503
Committed: Tue Jan 8 19:51:39 2008 UTC (11 years, 10 months ago) by filippis
Original Path: trunk/createGraphDb.sh
File size: 3310 byte(s)
Log Message:
createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned

!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added

!!!!AIGraph:
-getResidueSerial method added

RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field

DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.

testDbRIGraph added:
It reads one graph from a source db based either 
-on pdbcode, chaincode and graph properties or 
-on scop id and graph properties or 
-on a graph id 
and it writes the graph to a destination db.

Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence

CatalSiteSet:
- removeCatalSiteRes(int resser) method added

CatalyticSite:
-remRes(int resser) method added

Scop:
-remove(ScopRegion e) method added

genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.


Line User Rev File contents
1 filippis 409 #!/bin/sh
2     function usage {
3     echo
4     echo "Script to create/link/index a graph database. "
5     echo
6     echo "Usage: $1 -d <db_name> -m <mode>"
7     echo
8     echo "-d <db_name> the graph database name "
9     echo "-m <mode> create/index/unindex tables "
10     echo
11     }
12    
13     #
14     #Set default value for variables
15     #
16     graphDb=""
17     mode=""
18     h="white"
19    
20     while getopts d:m: opt
21     do
22     case "$opt" in
23     d) graphDb="$OPTARG";;
24     m) mode="$OPTARG";;
25     esac
26     done
27    
28     if [ -z "$graphDb" ] || [ -z "$mode" ]
29     then
30     echo "Missing or more arguments"
31     usage $0
32     exit 1
33     fi
34    
35     arch=`uname -m`
36     case "$arch" in
37     i686)
38     mysqldir=/project/tla/dist/mysql-i686
39     ;;
40     x86_64)
41     mysqldir=/project/tla/dist/mysql
42     ;;
43     *)
44     mysqldir=/project/tla/dist/mysql-i686
45     ;;
46     esac
47    
48     mysqlbin=$mysqldir/bin/mysql
49     master=white
50     db=test
51    
52     if [ "$mode" == "CREATE" ]
53     then
54     $mysqlbin -pnieve -h $h -B -N $db <<ENDSQL
55     SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
56     CREATE DATABASE IF NOT EXISTS ${graphDb}
57     DEFAULT CHARACTER SET latin1 DEFAULT COLLATE latin1_general_cs;
58     ENDSQL
59     $mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL1
60     SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
61     CREATE TABLE chain_graph LIKE abstract.chain_graph;
62 filippis 503 CREATE TABLE scop_graph LIKE abstract.scop_graph;
63 filippis 409 CREATE TABLE single_model_graph LIKE abstract.single_model_graph;
64     CREATE TABLE single_model_node LIKE abstract.single_model_node;
65     CREATE TABLE single_model_edge LIKE abstract.single_model_edge;
66     CREATE TABLE pdb_residue_info LIKE abstract.pdb_residue_info;
67    
68     ALTER TABLE chain_graph
69     MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
70 filippis 413 MODIFY pchain_code VARCHAR(2) NOT NULL,
71 filippis 409 MODIFY scops INT,
72     MODIFY caths INT,
73     MODIFY entry_id INT,
74     MODIFY assembly_id INT,
75     MODIFY chain_id INT,
76     MODIFY model_id INT;
77    
78 filippis 503 ALTER TABLE scop_graph
79     MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
80     MODIFY pchain_code VARCHAR(2) NOT NULL,
81     MODIFY sunid INT UNSIGNED,
82     MODIFY sccs VARCHAR(10),
83     MODIFY domain_type ENUM('UNKNOWN', 'WHOLECHAIN', 'SINGLEFRAGMENT', 'MULTIFRAGMENT', 'MULTICHAIN'),
84     MODIFY num_chain INT,
85     MODIFY num_fragment INT,
86     MODIFY caths INT,
87     MODIFY num_chain_res INT,
88     MODIFY chain_scops INT,
89     MODIFY entry_id INT,
90     MODIFY assembly_id INT,
91     MODIFY chain_id VARCHAR(35),
92     MODIFY model_id INT;
93    
94 filippis 409 ALTER TABLE single_model_graph
95     MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT;
96    
97     ALTER TABLE single_model_node
98 filippis 503 MODIFY num INT NOT NULL,
99 filippis 409 MODIFY ssid VARCHAR(5),
100     MODIFY sheet_serial CHAR(1);
101    
102     ALTER TABLE single_model_edge
103 filippis 503 MODIFY i_num INT NOT NULL,
104 filippis 409 MODIFY i_ssid VARCHAR(5),
105     MODIFY i_sheet_serial CHAR(1),
106 filippis 503 MODIFY j_num INT NOT NULL,
107 filippis 409 MODIFY j_ssid VARCHAR(5),
108     MODIFY j_sheet_serial CHAR(1);
109     ENDSQL1
110     fi
111    
112     if [ "$mode" == "INDEX" ]
113     then
114     $mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
115     SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
116     CREATE INDEX NODE_GRAPH_IDX ON single_model_node (graph_id);
117     CREATE INDEX EDGE_GRAPH_IDX ON single_model_edge (graph_id);
118 filippis 413 CREATE INDEX CHAIN_IDX ON pdb_residue_info (pdb_code, chain_code, pdb_chain_code);
119 filippis 409 ENDSQL
120     fi
121    
122     if [ "$mode" == "UNINDEX" ]
123     then
124     $mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
125     SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
126     DROP INDEX NODE_GRAPH_IDX ON single_model_node;
127     DROP INDEX EDGE_GRAPH_IDX ON single_model_edge;
128     ENDSQL
129     fi

Properties

Name Value
svn:executable *