Gscope Procedures

You'll find here description about some important Gscope Procedures

 see all procedures with Gscope Chez le Psy

proc StringInteractome

With a list of gene names, NM_xxxxxs, probeset_ids, etc. you'll get a STRING analysis as a set of files allowing the display of the network with Cytoscape

 Please see our wiki page for String

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]  
set Info [Iterator $Name    Get Total Iter]

GO

Attention attention ! Depuis 2014/12/6 j'ai mis "biological_process" "cellular_component" "molecular_function" en TermType. Du coup on récupère tout ... et peut-être trop. En plus ce n'est plus tellement compatible avec les mémorisation que je faisais avant un peu partout :'(

Ce qu'il faut savoir aussi c'est que la recherche des GO se fait en remontant vers les parents: quand un gène est à un noeud on le place artificiellement dans tous ses ancêtres.

proc GoGetInFile {File args}

Petite astuce qui consite à ranger le résulta de la commande args dasn un fichier ... ça nous évite de passer par Wscope au retour car GO2000 veut simplemnet créer le fichier pour s'en servir de mémoire tampon plus tard ... Désolé pour cet artifice.

proc GoNext {UpDown Go}

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

• GoNext returns its children if down, its parent if up (can be more than 1 parent)
• GoChildren Go is GoNext Down Go
• GoParents Go is GoNext Up Go

proc GoGetFromGo {Go GENEofPFAMwhatyouneed JoinCar RecordsJoinCar UpDown}

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

• UpDown can be Up / Down / Here / -n (n levels Up) / 0 (Here) / n (n levels down) ... and if it starts with + we skip 0 (+1 is only children)
• 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 ListOfGo           [GoGetFromGo "protein binding" GO]
set ListOfGoWithAcc    [GoGetFromGo "protein binding" GOacc]
set ListOfGoWithIdName [GoGetFromGo "GO:0005515"      GOid,name]
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 {Up ""}}

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

• GoGetFromGene returns what you need about all its GO

if Up == "Up" each geen is also included recursilvely in the parent GOs

set ListOfGO           [GoGetFromGene PAX6 GO]
set ListOfGOWithAcc    [GoGetFromGene PAX6 GOacc]
set ListOfGOWithName   [GoGetFromGene PAX6 GOacc,name]
set ListOfGOWithSource [GoGetFromGene PAX6 GOacc,a.source_db_id]

proc GoGetFromGeneList {List GOwhatyouneed JoinCar RecordsJoinCar ListJoinCar {Up ""}}

Same as GoGetFromGene but for a list of genes. The return value is an indexed list of couples {gene=itsGOs} {gene=itsGOs} ...

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           [GoGetFromPfam PF09088 GO]
set ListOfGOWithAcc    [GoGetFromPfam PF09088 GOacc]
set ListOfGOWithName   [GoGetFromPfam PF09088 GOacc,name]
set ListOfGOWithSource [GoGetFromPfam PF09088 GOacc,a.source_db_id]