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 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]