invalid command name "global_variables"

2005-10-18
2013-04-18
  • Tom Isenbarger
    Tom Isenbarger
    2005-10-18

    I am trying to use the following naming scheme file for a directed assembly.  I have short (1-2 Mbp) clones for which I have end sequences (using TOPO kit and T3 and T7 primers to generate sequence) and I want to assemble the pairs of sequences.  I was told to use this naming scheme file (below).  At first, when in pregap4 I loaded this file using File:Load Naming Scheme, I was receiving the error "invalid command name "naming_scheme"".  After removing some of the comments in the file, now I get the message in the subject.

    Any help?

    Thanks,
    Tom Isenbarger

    [naming_scheme]
    #
    # This is a general purpose naming scheme for mutation detection purposes.
    # It sets the TN and PR records in the experiment file. An 'f' or 'r' suffix
    # on the name indicates the sequence direction, forward or reverse.
    #
    set ns_name "Mutation detection naming scheme"
    set ns_regexp {(.*)\.(T3|T7)(.)$}
    set ns_lt(TN) {$1}
    set ns_lt(PR) {subst {$3 {[fF] 1} {[rR] 2} 0}}
    set_name_scheme

    # Generates AP lines for directed assembly
    proc AP_com {} {
        global lines
        if {[string match *T3f $lines(ID)]} {
            return "*new* 0 0 0"
        } else {
        regsub "\.T7r" $lines(ID) ".T3f" sibling
        return "$sibling - -50 1400"
        }
    }

    [global_variables]

    proc AP_com {} {
        global lines
        if {[string match *T3f $lines(ID)]} {
            return "*new* 0 0 0"
        } else {
        regsub "\.T7r" $lines(ID) ".T3f" sibling
        return "$sibling - -50 1400"
        }
    }
    proc PR_com {} {    global lines
        if {[regexp {(.*)\.(T3|T7)(.)$} $lines(ID) matched 1 2 3] == 0} {
            return ""
        }
        if {[string match {[fF]} $3]} {return 1}
        if {[string match {[rR]} $3]} {return 2}
        return 0
    }
    proc TN_com {} {    global lines
        if {[regexp {(.*)\.(T3|T7)(.)$} $lines(ID) matched 1 2 3] == 0} {
            return ""
        }
        return $1
    }

     
    • James Bonfield
      James Bonfield
      2005-10-27

      I'm not sure why you're getting these errors. Does your naming scheme file contain all of what you've quoted, or is tat the pregap4 config file?

      The naming scheme file should ONLY contain the [naming_scheme] header along with the set_ns* and set_name_scheme lines. See the examples in $STADENROOT/lib/pregap4/naming_schemes.

      James