bugs, idmapping

src/ordali_StrucObj.tcl

@@ -31,9 +31,13 @@ proc SetupPDBObject {} {
 	# Arguments
 	# - nom : file or text or lines or id
 	# - init : 1 -> load from db, 0 load fram <nom>
-	if {$init eq ""} {set init 0}
+	if {$init eq ""} {
+	    set init 0
+	}
 	# - InDb : 1 store in db, 0 don't
-	if {$InDb eq ""} {set InDb 1}
+	if {$InDb eq ""} {
+	    set InDb 1
+	}
 
 	if {$init} {
 	    my UpdateFromDB
@@ -48,7 +52,11 @@ proc SetupPDBObject {} {
 		set src "list"
 	    } elseif {[file extension $nom] eq ""} {
 		#set Llignes [RecupereUnFichierSurWeb [string toupper $nom]]
-		set textePDB [TextePDB [string toupper $nom] ALL "" "OnTheWeb"]
+		package require TclCurl
+		set url "https://files.rcsb.org/download/XXXX.pdb"
+		regsub -all "XXXX" $url $nom url
+		curl::transfer -url $url -bodyvar textePDB
+		#set textePDB [TextePDB [string toupper $nom] ALL "" "OnTheWeb"]
 		set Llignes [split $textePDB \n]
 		if {$Llignes eq "ERREUR" || $Llignes eq ""} {
 		    return 0

src/ordali_admin.tcl

@@ -664,6 +664,23 @@ proc MyProc {name argList body} {
 }
 
 
+proc DoMacPack {} {
+    cd /home/moumou
+
+    catch {file delete -force {*}[glob macpack*]}
+    file copy ./ordali/src/macpack.tcl .
+    exec ./tclkit sdx.kit qwrap  macpack.tcl
+    exec ./tclkit sdx.kit unwrap macpack.kit
+    cd macpack.vfs
+    file copy -force ~/ordali/Build/macosx-x86_64 .
+    cd ..
+    exec ./tclkit sdx.kit wrap macpack -runtime mackit
+
+    exit
+}
+
+
+
 
 
 # http://kitcreator.rkeene.org/kitcreator

src/ordali_misc.tcl

@@ -13477,3 +13477,104 @@ proc cherie {} {
     return
 }
 
+
+proc tseb {} {
+    package require Rtcl
+    
+    set Ll [LesLignesDuFichier mat.dst]
+    set vals [concat {*}$Ll]
+    Rpipe "x   <- c([join $vals ,])"
+    Rpipe "mat <- matrix(x,byrow=T,nrow=5, ncol=5)"
+    Rpipe "res <- eigen(x)"
+    
+    return
+}
+
+
+proc MakeTransparentImage {img} {
+    LoadTkAndPackages
+    
+    set id [image create photo -file $img]
+    set col {255 255 255}
+    set wdt [image width $id]
+    set hgt [image height $id]
+    for {set x 0} {$x < $wdt} {incr x} {
+	for {set y 0} {$y < $hgt} {incr y} {
+	    if {[$id get $x $y] == $col} {
+		$id transparency set $x $y 1
+	    }
+	}
+    }
+    
+    $id write [file rootname $img].png
+
+    return
+}
+
+
+proc thom {} {
+    global db
+    
+    set La [IDMapping_sql GENE_NAME ACC zufsp]
+    puts "La [llength $La]"
+    set La [lindex $La 0]
+    puts "La [llength $La]"
+    set Lh [IDMapping_sql ACC NCBI_TAXID $La]
+    puts "Lh [llength $Lh]"
+    
+    set Lix [lsearch -all -exact $Lh "9606"]
+    foreach ix $Lix {
+	puts "human  : ix=$ix [lindex $La $ix]"
+    }
+
+    set Ld [IDMapping_sql GENE_NAME NCBI_TAXID zufsp]
+    puts "\nLd [llength $Ld]"
+    set Ld [lindex $Ld 0]
+    set Lix [lsearch -all -exact $Ld "9606"]
+    foreach ix $Lix {
+	puts "direct ix=$ix [lindex $Ld $ix]"
+    }
+
+    set La [IDMapping_sql GENE_NAME ACC zufsp 9606]
+    puts "La $La"
+
+    set Lf [IDMapping_sql GENE_NAME GENE_SYNONYM zufsp 9606]
+    puts "\nLf $Lf\n"
+    
+    cd /commun/bics/IDMapping/production/SQLDBS
+
+    puts "\nDeux etapes"
+    set Lh [IDMapping_sql GENE_NAME ACC zufsp 9606]
+    set Lh [lindex $Lh 0]
+    puts "[llength $Lh] $Lh"
+    set Lh [IDMapping_sql ACC GENE_SYNONYM $Lh]
+    puts "$Lh"
+
+    set taxid 9606
+    set Lid zufsp
+    set Lacc zufsp
+    set BankSource GENE_NAME
+    set BankTarget GENE_SYNONYM
+    
+    set db [DbIDMappingSQL GENE_NAME open]
+    AttachIDMappingBank GENE_SYNONYM
+    AttachIDMappingBank NCBI_TAXID
+
+
+    #set cmd "WITH db1(id) AS (VALUES ('[join $Lid '),(']')) select db1.id, db2.id from $BankSource as db1, $BankTarget as db2, NCBI_TAXID as db3 where db1.id in ('[join $Lacc ',']') and db3.id = '$taxid' and db1.acc = db2.acc and db2.acc = db3.acc"
+    
+    #set cmd "WITH tmp(acc) AS (VALUES ('[join $Lacc '),(']')) SELECT tax.acc,tax.id FROM tmp AS dbin, NCBI_TAXID AS tax WHERE tax.acc = dbin.acc and tax.id = '$taxid'"
+
+    set cmd "select db1.id, db2.id from GENE_NAME as db1, GENE_SYNONYM as db2, NCBI_TAXID as db3 where db1.id in ('ZUFSP') and db1.acc = db2.acc and db2.acc = db3.acc and db3.id = '9606'"
+    
+    #set cmd "select db1.id, db2.id from GENE_NAME as db1, GENE_SYNONYM as db2, NCBI_TAXID as db3 where db1.id='ZUFSP' and db1.acc = db2.acc and db2.acc = db3.acc and db3.id = '9606'"
+    puts "cmd= $cmd"
+    set Lres [$db eval $cmd]
+    puts "Lres $Lres"
+    
+
+
+    exit
+}
+
+    

src/ordali_sequence.tcl

@@ -3125,29 +3125,42 @@ proc Reigen {} {
     foreach a $Ln {
 	set tmp {}
 	foreach b $Ln {
-	    lappend tmp [lindex $TDesPCI($a,$b) 0]
+	    lappend tmp [expr {1.0 - [lindex $TDesPCI($a,$b) 0]}]
 	}
 	lappend m $tmp
     }
-
+    lmap x $m {plist $x %6.4f}
+    puts ""
     package require Rtcl
-
+    
     Rpipe "x <- c([join [concat {*}$m] ,])"
     Rpipe "x <- matrix(x, byrow = T, ncol=5, nrow=5)"
     
-    Rpipe "res <- eigen(x, symmetric=TRUE)"
+    #Rpipe "res <- eigen(x, symmetric=TRUE)"
+    Rpipe "res <- eigen(x)"
 
     set val [::rtcl::getvalue "res\$values"]
-    set vec [lrange [::rtcl::getvalue "res\$vectors"] 0 4]
-    
     puts "val :"
     plist $val %6.3f
     set sum [::tcl::mathop::+ {*}$val]
-    puts "sum= $sum"
+    puts "sum = $sum"
 
     puts "vec :"
-    plist $vec %6.3f
+    set k 0
+    set Lvec [::rtcl::getvalue "res\$vectors"]
+    while {$k < 25} {
+	set vec [lrange $Lvec $k $k+4]
+	incr k 5
+	
+	plist $vec %6.3f
+    }
+    puts ""
 
+    set vec [lrange $Lvec 0 4]
+    set sum [+ {*}$vec]
+    set new [lmap x $vec {expr {$x/$sum}}]
+    plist $new %6.3f
+    
     return $vec
 }