Difference between revisions of "Gscope Procedures"

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Several procs are concerned ... see the source file [http://lbgi.igbmc.fr/gag/cgi-bin/GscopeServer?EVImm&FicheMoi&rR/gscope/gscope_go.tcl gscope_go.tcl]  
 
Several procs are concerned ... see the source file [http://lbgi.igbmc.fr/gag/cgi-bin/GscopeServer?EVImm&FicheMoi&rR/gscope/gscope_go.tcl gscope_go.tcl]  
 
See the source file [http://lbgi.igbmc.fr/gag/cgi-bin/GscopeServer?Zero&AfficheLaProc&GoGetFromPfam proc GoGetFromPfam]
 
See the source file [http://lbgi.igbmc.fr/gag/cgi-bin/GscopeServer?Zero&AfficheLaProc&GoGetFromPfam proc GoGetFromPfam]
GoGetFromGene returns ''what you need'' about all its GO
+
* GoGetFromGene returns ''what you need'' about all its GO
 
<source lang="tcl">
 
<source lang="tcl">
 
set ListOfGO          [GoGetFromFromPfam PF09088 GO]
 
set ListOfGO          [GoGetFromFromPfam PF09088 GO]

Revision as of 11:22, 25 April 2009

You'll find here description about Gscope Procedures

 see all procedures with Gscope Chez le Psy

proc Iterator

See the source of proc Iterator

set Name [Iterator New Init $L0 $L1 $L2]
while {[Iterator $Name Next  v0  v1  v2]} { ... } #rR sans $
#rR L2 is the fastest !!!!!!!!!!!!!!!!!!!!
#rR Attention lists are numbered from 0 to 2 (for the caller)
#rR           but are from 2 to 0 in the proc
Iterator $Name Reset
Iterator $Name Destroy
set Info [Iterator Iterator Get ListOf Name]
set Info [Iterator $Name    Get Current 2]    #rR current index de L2
set Info [Iterator $Name    Get Current All]  #rR tous les current L0 L1 L2
set Info [Iterator $Name    Get Max 0]
set Info [Iterator $Name    Get Max All]

proc GoGetFromGo {Go GENEofPFAMwhatyouneed JoinCar RecordsJoinCar}

Several procs are concerned ... see the source file gscope_go.tcl See the source file proc GoGo

  • GoGetFromGo starts from a GO and includes recursively all its children (ATTENTION we use Mus musculus by default) and return what you need about its GENEs or PFAMs
set ListOfPfam         [GoGetFromGo "protein binding" PFAM]
set ListOfPfamWithId   [GoGetFromGo "protein binding" PFAMxref_key,id]
set ListOfPfamWithDesc [GoGetFromGo "GO:0005515"      PFAMxref_key,xrefdesc]
set ListOfGene         [GoGetFromGo "protein binding" GENE]
set ListOfGene         [GoGetFromGo "protein binding" GENEsymbol]
set ListOfGeneWithDesc [GoGetFromGo "GO:0005515"      GENEfull_name,symbol]

proc GoGetFromGene {Gene GOwhatyouneed JoinCar RecordsJoinCar}

Several procs are concerned ... see the source file gscope_go.tcl See the source file proc GoGetFromPfam

  • GoGetFromGene returns what you need about all its GO
set ListOfGO           [GoGetFromGene PAX6 GO]
set ListOfGOWithAcc    [GoGetFromFromGene PAX6 GOacc]
set ListOfGOWithName   [GoGetFromFromGene PAX6 GOacc,name]
set ListOfGOWithSource [GoGetFromFromGene PAX6 GOacc,a.source_db_id]

proc GoGetFromPfam {Pfam GOwhatyouneed JoinCar RecordsJoinCar}

Several procs are concerned ... see the source file gscope_go.tcl See the source file proc GoGetFromPfam

  • GoGetFromGene returns what you need about all its GO
set ListOfGO           [GoGetFromFromPfam PF09088 GO]
set ListOfGOWithAcc    [GoGetFromFromPfam PF09088 GOacc]
set ListOfGOWithName   [GoGetFromFromPfam PF09088 GOacc,name]
set ListOfGOWithSource [GoGetFromFromPfam PF09088 GOacc,a.source_db_id]