name        "PATSER - Sequence vs. matrix"
tip    "Score the match of a sequence with an alignment matrix"
system
    solaris    sparc
var "matfile"
    type        text
    label       "Matrix file"
    default     "none"
var "in1"
    type        tempfile
    direction   in
    format      genbank
    save        true
var "preedit"
    type        chooser
    label       "Edit alphabet file?"
    default     1
    choices
        "Yes"       "$BL_TextEditor %in1%.conseq.alphabet;"
        "No"        ""
panel
    var "Run"
        type        button
        label       "Run"
        shell       "(readseq %in1% -pipe -form=Pearson | fasta-consensus > %in1%.conseq; cp $BIRCH/dat/Consensus/alphabet.dat %in1%.conseq.alphabet; cp %MATFILE% %in1%.conseq.mat; %PREEDIT% patser.csh %in1%.conseq %in1%.conseq.mat %in1%.patout; ($BL_TextEditor %in1%.patout;rm %in1%.patout)& rm %in1% %in1%.conseq*) "
        close       true
    var "Help"
        type        button
        label       "Help"
        shell       "$BIRCH/script/chooseviewer.py $BIRCH/doc/Consensus/patser.asc"
        close       false