couldn't read file "../src/ordali_web.tcl": no such file or directory
    while executing
"source ../src/ordali_web.tcl"
    (in namespace eval "::request" script line 3)
    invoked from within
"namespace eval ::request $script"
    ("::try" body line 12)
OUTPUT BUFFER:
#package require http
#package require dom::tcl
source ../src/ordali_web.tcl
source ../src/ordali_services.tcl
package require http
package require tdom


proc eSummaryREST_old {db Lid} {
    set url "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
    # eSummary with db=protein only accepts GI numbers
    #
    # proceed by 10 000 ids batches
    set Lres [list]
    set i 0
    set lg [llength $Lid]
    while {$i < $lg} {
	set Ln [lrange $Lid $i $i+9999]	
	set query [::http::formatQuery \
		db $db \
		id [join $Lid ,] \
		retmax 10000]
	set ddb [HttpCopy $url "" $query]
	#set ddb [eSummaryProcessXML $ddb]
	incr i 10000
    }

    return $ddb
}



set Lnm [list 256819652 228471929 188994130]
#puts "[eSummaryREST protein $Lnm]"

set Lnm [list XM_001241671.1 NC_008609.1]
set Lnm NC_008609
set Lnm XM_001241671.1
set Lnm XM_001267187.1


proc handle_start {name attributes args} {
    puts "start $name"
  set ::CurrentTag $name
};# handle_start

proc handle_end {name args} {
  set ::CurrentTag {}
};# handle_end


proc ExtraitRNA {Lxml refseq prot} {
    set Rdoc [::dom::tcl::parse $Lxml]
    set rna "" ; set found 0

    set pid ""
    set Lkey [$Rdoc selectNode //key]
    foreach Nk $Lkey {
	if {[$Nk selectNode string(.)] ne "CDS"} {
	    continue
	}
	set nd $Nk ; set ns "" ; set is 0
	while {[set ns [$nd nextSibling]] ne $nd} {
	    puts "  $is [$nd nodeName]"
	    if {[$nd nodeName] eq "location"} {
		set loc [$nd selectNode string(.)]
	    }
	    if {[$nd nodeName] eq "quals"} {
		puts "break $nd"
		break
	    }
	    set nd $ns
	    incr is
	}
	set nqf [$nd firstChild]
	puts "loc $loc | [$nqf nodeValue]"
	foreach nd [$nqf childNodes] {
	    puts "[$nd nodeName] [$nd selectNode string(.)]"
	    if {[$nd nodeName] eq "name" && [$nd selectNode string(.)] eq "protein_id"} {
		set nv [$nd nextSibling]
		set pid [$nv selectNode string(.)]
		break
	    }
	}
	if {$pid ne "" && [regexp -nocase $prot $pid]} {
	    set found 1
	    break
	}
    }
    if {$found} {
	set Nrna [$Rdoc selectNodes //sequence]
	if {$Nrna ne ""} {
	    set seq [$Nrna selectNode string(.)]
	    set rna [ExtractRNAFromSeqGivenLoc $seq $loc]
	} else {
	    set rna ""
	}
    }
    $doc delete

    return $rna
}



#puts "rna [ExtraitRNA $xml XM_001241671.1 toto]"


## Parse the xml data...
#xml parsechannel $fd
#xml parse $xml

## Done! Free parser and close file...
#close $fd
#xml free 





proc parse {xml target} {
    puts "start parsing"
    set ::S {}
    set ::pt(inKey) 0
    set ::pt(target) $target
    set ::pt(readV) 0
    set ::pt(seq) ""
    set p [expat \
	    -elementstartcommand el \
	    -characterdatacommand  ch \
	    -elementendcommand  ee ]
    if [catch {$p parse $xml} res] {
        puts "Error: $res"
    }
}
#---- Callbacks for start, end, character data
proc el {name atts} {
    lappend ::S $name ;# push
    if {$name eq "GBFeature_key"} {set ::pt(inKey) 1}
}
proc ee {name} {
    set ::S [lrange $::S 0 end-1] ;# pop
    if {$name eq "bar"} {
        puts $g(grill)=$g(baz) 
    }
}
proc ch {str} {
    set type [lindex $::S end]
    if {! $::pt(inKey)} {return}
    
    switch $type {
	GBFeature_key {
	    if {$str ne "CDS"} {
		set ::pt(inKey) 0
	    }
	}
	GBFeature_location {
	    set ::pt(currLoc) $str
	}
	GBQualifier_name {
	    if {$str eq "protein_id"} {
		set ::pt(readV) 1
	    }
	}
	GBQualifier_value {
	    if {$::pt(readV)} {
		if {[regexp -nocase "$::pt(target)" $str]} {
		    set ::pt(id) $str
		    set ::pt(readV) 0
		    set ::pt(loc) $::pt(currLoc)
		}
	    }
	}
	GBSeq_sequence {
	    set ::pt(seq) $str
	}
    }
}


proc eFetchREST {db Lid what} {
    set url "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
    
    switch $db {
	"protein" {
	    set rettype gp
	    set retmode xml
	}
	"nucleotide" {
	    set rettype fasta_cds_na
	    set retmode text
	}
    }
    set query [::http::formatQuery \
	    db $db \
	    id [join $Lid ,] \
	    rettype $rettype \
	    retmode $retmode]
    set ddb [HttpCopy $url "" $query]

    return $ddb
}

proc eLinkREST {dbfrom dbto Lid {cmd ""}} {
    set url "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi"
    set Lres [list]
    set i 0
    set lg [llength $Lid]
    while {$i < $lg} {
	set Ln [lrange $Lid $i $i+9999]	
	if {$cmd ne ""} {
	    set Tcmd cmd
	} else {
	    set Tcmd ""
	}
	
	set query [::http::formatQuery \
		dbfrom $dbfrom \
		db $dbto \
		id [join $Ln ,] \
		$Tcmd $cmd]
	set xml [HttpCopy $url "" $query]

	puts "$query"
	puts "$xml"
	lappend Lres {*}[eLinkProcess $xml ngb]

	incr i 10000
    }
    puts "Lres $Lres"
    set ret [list]
    if {$Lres != {} } {
	set aT [eSummaryREST $dbto $Lres]
	array set T $aT
	foreach {a v} [array get T "*,refseq"] {
	    lappend ret $v
	}
    }

    return $ret
}

#set Ltx [list 313627 314230 699218]
set nm 135102
#puts "[eSummaryREST protein $nm]"
#exit

set nm [list 257790368 226291546 291176984 150866285]
set nm 135102
#puts "[eLinkREST protein protein $nm ncheck]"
puts ""
puts "[eLinkREST protein protein $nm neighbor_score]"
exit

#set nm XP_455053.1
set nm NC_001148.4
set nm XP_001241672
puts "[eFetchREST protein $nm cds]"
exit

set gi 169773541
set acc NC_012860.1
set res [eFetchREST nucleotide $acc]
puts "$res"
exit

puts "Lnuc $Lnuc"
exit

set Lnm NC_001148.4
set Lnm xp_001241672
set xml [eFetchREST protein $Lnm]
puts "$xml"
parse $xml NP_015221.1
parray pt