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