Updated 2005-02-22 16:04:22 by lwv

DESCRIPTION

Snittype for getting information from LocusLink-IDs [1]. Currently you just download the files from: ftp://ftp.ncbi.nih.gov/refseq/LocusLink/ . We assume that you download: ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL.out_hs.gz and for GeneOntology mappings: ftp://ftp.ncbi.nih.gov/refseq/LocusLink/loc2go . In the future downloading may be done via http::geturl directly from the package. Candiate for future biotcl package.
 #  Author        : Dr. Detlef Groth, MPIMG Berlin
 #  Created By    : Dr. Detlef Groth
 #  Created       : Fri Feb 18 13:06:07 2005
 #  Last Modified : <050222.0622>
 #
 #  Description	  : snittype for getting informations for LocusLink-IDs.
 #
 package require snit 0.97
 package require oomk

 snit::type LocusLinkFile {
    option -filename ""
    option -mkfile ""
    option -gofile ""
    variable db
    variable dbgo
    variable pvLocusLink
    # `LocusLinkFile llf -filename LL.out_hs ?-mkfile metakitfile?' --
    #            constructor for the LocusLinkFile type
    #  Arguments:
    #           `-filename filename' the LocusLink file from ftp://ftp.ncbi.nih.gov/refseq/LocusLink/
    #           `?-mkfile?' the metakit databasefile, defaults to filename.mk
    # -----------------------------------------------
    constructor {args} {
        $self configurelist $args
        if {$options(-mkfile) eq ""} {
            set options(-mkfile) $options(-filename).mk
        }
        if {$options(-gofile) eq ""} {
            set options(-gofile) [file join [file dirname $options(-filename)] LOC2GO]
        }
        set db [mkstorage %AUTO% $options(-mkfile)]
        if {[file size $options(-mkfile)] < 2} {
            $self CreateMkDB
        } else {
            [$db view locuslink] as pvLocusLink
        }

        if {[file exists $options(-gofile)] && (![file exists $options(-gofile).mk] || [file size $options(-gofile).mk] < 2)} {
            set dbgo [mkstorage %AUTO% $options(-gofile).mk]
            $self CreateGoDB

        }
    };
    destructor {
        $db close
        catch {$dbgo close}
    }
    # public methods (are lowercase)
    # `llf' getInfo -key value ?-mode exact|glob? --
    #          get info for a certain key might be one of id,symbol, chr or descr), from the LocusLinkDB
    #  Arguments:
    #          `key' the property to search for
    #  Returns:
    #          list of list where each list contains key/value pairs from the database
    # ------------------------------------------------------------
    method getInfo {key val args} {
        regsub -- {-} $key "" colkey
        #puts "colkey $colkey val $val"
        set arg(-mode) exact
        array set arg $args
        [$pvLocusLink select -$arg(-mode) $colkey $val] as pSel
        set res [list]
        if {[$pSel size] > 0} {
            $pSel loop c { lappend res [array get c] }
        }
        return $res
    }
    method getGos {key val} {
        error "method getGOs is not yet implemented"
    }

    # private Methods
    method CreateGoDB {} {
        if [catch {open $options(-gofile) r} infh] {
            puts stderr "Cannot open $options(-gofile): $infh"
            return 0
        } else {
            $dbgo layout goinfo {id:I go quality}
            [$dbgo view goinfo] as pvGO
            set x 0
            set prog [Progress %AUTO% -file $options(-gofile)]
            puts stderr "Converting $options(-gofile)"
            while {[gets $infh line] >= 0} {
                set F [split $line \t]
                if {[expr $x % 1000] == 0} { $prog progress [tell $infh] }
                $pvGO append id [lindex $F 0] go [lindex $F 1] quality [lindex $F 2]
            }
            close $infh
            $dbgo commit
        }
    }
    method CreateMkDB {} {
        if [catch {open $options(-filename) r} infh] {
            puts stderr "Cannot open $options(-filename): $infh"
            return 0
        } else {
            $db layout locuslink {id symbol chr chrpos descr}
            [$db view locuslink] as pvLocusLink
            set prog [Progress %AUTO% -file $options(-filename)]
            set x 0
            while {[gets $infh line] >= 0} {
                set F [split $line \t]
                if {[expr $x % 100] == 0} { $prog progress [tell $infh] }
                $pvLocusLink append id [lindex $F 0] symbol [lindex $F 1] chr [lindex $F 4] \
                          chrpos [lindex $F 5] descr [lindex $F 6]
            }
            close $infh
            $db commit
            #$db close

        }
    };

 }
 proc test {} {
    source [file join [file dirname [info script]] Progress.tcl]
    set file LL.out_hs
    set sf [LocusLinkFile %AUTO% -filename /project/goblet/data/LocusLink/$file]
    puts  [$sf getInfo -id 1]
    puts  [$sf getInfo -symbol AANAT]
    puts  [$sf getInfo -chrpos 2q31]
    puts  [llength [$sf getInfo -chr X]]
    puts [$sf getInfo -descr "interleukin*receptor*" -mode glob]

 }

Category Science