Changeset 419

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Timestamp:
06/25/10 22:54:46 (20 months ago)
Author:
AlexanderPico
Message:

updating unique Sc handling

Files:
1 modified

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  • trunk/dbbuilder/src/org/bridgedb/build/scripts/buildPathVisio.sh

    r376 r419  
    1414## Special modification for Yeast database: swapping in SGD identifiers from external file 
    1515if [[ $DatabaseSpecies == Sc ]]; then 
    16         rm ${ScriptsDir}/registry.genenames.tab 
    17         wget http://downloads.yeastgenome.org/gene_registry/registry.genenames.tab 
    18         mv registry.genenames.tab ${ScriptsDir}/. 
     16        rm ${ScriptsDir}/SGD_features.tab 
     17        wget http://downloads.yeastgenome.org/chromosomal_feature/SGD_features.tab 
     18        mv SGD_features.tab ${ScriptsDir}/. 
    1919        ${mysql} -e "create table ${DatabaseCS}.sgd (a varchar(31), b varchar(31), c varchar(31), d varchar(31), e varchar(31), f varchar(31), g varchar(31))"; 
    20         ${mysql} -e "load data local infile '${ScriptsDir}/registry.genenames.tab' into table ${DatabaseCS}.sgd fields terminated by '\t' lines terminated by '\n'"; 
    21         ${mysql} -e "create index i_a on ${DatabaseCS}.sgd (a)"; 
    22         ${mysql} -e "update ${DatabaseCS}.gene, ${DatabaseCS}.sgd set ${DatabaseCS}.gene.ID = ${DatabaseCS}.sgd.g where ${DatabaseCS}.gene.Symbol = ${DatabaseCS}.sgd.a and ${DatabaseCS}.gene.Code = 'D'"; 
    23         ${mysql} -e "update ${DatabaseCS}.attr, ${DatabaseCS}.sgd set ${DatabaseCS}.attr.ID = ${DatabaseCS}.sgd.g where ${DatabaseCS}.attr.Value = ${DatabaseCS}.sgd.a and ${DatabaseCS}.attr.Code = 'D'"; 
     20        ${mysql} -e "load data local infile '${ScriptsDir}/SGD_features.tab' into table ${DatabaseCS}.sgd fields terminated by '\t' lines terminated by '\n'"; 
     21        #${mysql} -e "create index i_a on ${DatabaseCS}.sgd (a)"; 
     22        ${mysql} -e "update ${DatabaseCS}.gene, ${DatabaseCS}.sgd set ${DatabaseCS}.gene.ID = ${DatabaseCS}.sgd.d where ${DatabaseCS}.gene.Symbol = ${DatabaseCS}.sgd.a and ${DatabaseCS}.gene.Code = 'D'"; 
     23        ${mysql} -e "update ${DatabaseCS}.attr, ${DatabaseCS}.sgd set ${DatabaseCS}.attr.ID = ${DatabaseCS}.sgd.d where ${DatabaseCS}.attr.Value = ${DatabaseCS}.sgd.a and ${DatabaseCS}.attr.Code = 'D'"; 
    2424        ${mysql} -e "alter table ${DatabaseCS}.link add column (ID_Right2 varchar(31))"; 
    2525        ${mysql} -e "update ${DatabaseCS}.link set ID_Right2 = ID_Right where Code_Right = 'D'"; 
    26         ${mysql} -e "update ${DatabaseCS}.link, ${DatabaseCS}.sgd set ${DatabaseCS}.link.ID_Right = ${DatabaseCS}.sgd.g where ${DatabaseCS}.link.ID_Right2 = ${DatabaseCS}.sgd.a and ${DatabaseCS}.link.Code_Right = 'D'"; 
     26        ${mysql} -e "update ${DatabaseCS}.link, ${DatabaseCS}.sgd set ${DatabaseCS}.link.ID_Right = ${DatabaseCS}.sgd.d where ${DatabaseCS}.link.ID_Right2 = ${DatabaseCS}.sgd.a and ${DatabaseCS}.link.Code_Right = 'D'"; 
    2727        ${mysql} -e "alter table ${DatabaseCS}.link drop column ID_Right2"; 
    2828fi