/usr/share/staden/etc/siprc is in staden-common 2.0.0+b11-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Packages required
#-----------------------------------------------------------------------------
#-----------------------------------------------------------------------------
# Misc
#-----------------------------------------------------------------------------
#put somewhere else eventually.....
set_def SEQ.FILE.BUTTON.1 "Personal file"
set_def SEQ.FILE.BUTTON.2 "Sequence library"
set_def SEQ.FILE.NAME "Select source of sequence"
set_def SEQ.FILE.VALUE "2"
set_def SEQ.PERS.BUTTON.1 "Staden"
set_def SEQ.PERS.BUTTON.2 "EMBL"
set_def SEQ.PERS.BUTTON.3 "GenBank"
set_def SEQ.PERS.BUTTON.4 "PIR"
set_def SEQ.PERS.BUTTON.5 "GCG"
set_def SEQ.PERS.BUTTON.6 "FASTA"
set_def SEQ.PERS.NAME "Select file format"
set_def SEQ.PERS.VALUE "1"
#-----------------------------------------------------------------------------
# Global variables
#-----------------------------------------------------------------------------
#default protein score matrix
set_def SIP.PROT_MAT "$env(STADTABL)/pam250"
#-----------------------------------------------------------------------------
# Window sizes
#-----------------------------------------------------------------------------
set_def SIP.SEQ_DISP.PLOT_WIDTH 80
set_def SIP.RASTER.PLOT_HEIGHT 400
set_def SIP.RASTER.PLOT_WIDTH 400
set_def SIP.RULER.PLOT_HEIGHT 40
set_def SIP.RULER.PLOT_WIDTH 100
set_def RASTER.PLOT_HEIGHT 400
set_def RASTER.PLOT_WIDTH 400
set_def RASTER.BORDERWIDTH 2
set_def RASTER.TITLE "SPIN Sequence Comparison Plot"
set_def RULER.PLOT_HEIGHT 40
set_def RULER.PLOT_WIDTH 100
#-----------------------------------------------------------------------------
# Window names
#-----------------------------------------------------------------------------
set_def SIP.WIN .sip
set_def RASTER.WIN .raster
set_def RASTER.R.WIN .raster.r
set_def SIP.SEQ_DISP.WIN .sequence_display
#-----------------------------------------------------------------------------
#cursor
#-----------------------------------------------------------------------------
set_def SIP.CURSOR.SENSITIVE 5
set_def SIP.CURSOR.LINE_WIDTH 2
#-----------------------------------------------------------------------------
# initial settings
#-----------------------------------------------------------------------------
#expected number of matches for setting default cutoff score
set_def SIP.NUM_MATCHES 500
#max number of matches
set_def SIP.MAX_MATCHES 50000
#-----------------------------------------------------------------------------
# Useful common questions - asked by many options
#-----------------------------------------------------------------------------
set_defx defs_f_or_l_in WHICH.NAME "Input from"
set_defx defs_f_or_l_in WHICH.BUTTONS {list file}
set_defx defs_f_or_l_in WHICH.VALUE 2
set_defx defs_f_or_l_in NAME.NAME "List or file name"
set_defx defs_f_or_l_in NAME.BROWSE "Browse"
set_defx defs_f_or_l_in NAME.VALUE ""
set_defx defs_win_len NAME "window length"
set_defx defs_win_len VALUE "11"
set_defx defs_win_len MIN "1"
set_defx defs_win_len MAX "401"
set_defx defs_word_len NAME "word length"
set_defx defs_word_len DNA.VALUE "8"
set_defx defs_word_len DNA.MIN "1"
set_defx defs_word_len DNA.MAX "1000"
set_defx defs_word_len PROTEIN.VALUE "2"
set_defx defs_word_len PROTEIN.MIN "1"
set_defx defs_word_len PROTEIN.MAX "3"
set_defx defs_min_score NAME "minimum score"
#-----------------------------------------------------------------------------
# Our options
#-----------------------------------------------------------------------------
#compare spans
set_def SIP.CS.DIR.BUTTON.1 "reverse"
set_def SIP.CS.DIR.BUTTON.2 "forward"
set_def SIP.CS.DIR.NAME "direction"
set_def SIP.CS.DIR.VALUE "2"
set_def SIP.CS.RANGE_H.NAME "Horizontal"
set_def SIP.CS.RANGE_V.NAME "Vertical"
set_def SIP.CS.WIN_LEN $defs_win_len
set_def SIP.CS.MIN_SCORE $defs_min_score
set_def SIP.CS.LINE_WIDTH 0
set_def SIP.CS.COLOUR "#ff0000"; #red
set_def SIP.CS.SIMILAR.NAME "plot similar characters"
set_def SIP.CS.SIMILAR.VALUE 0
set_def SIP.CS.SCORE.NAME "character score"
set_def SIP.CS.SCORE.VALUE 1
set_def SIP.INFILE $defs_f_or_l_in
set_def SIP.INFILE.WHICH.NAME "Input reading names from"
#identity algorithm
set_def SIP.IDENTITY.WORD_LEN $defs_word_len
set_def SIP.IDENTITY.LINE_WIDTH 0
set_def SIP.IDENTITY.COLOUR "#0000ff"; #blue
#quick scan
set_def SIP.QS.WIN_LEN $defs_win_len
set_def SIP.QS.MIN_SCORE $defs_min_score
set_def SIP.QS.WORD_LEN $defs_word_len
set_def SIP.QS.SD.NAME "minimum sd"
set_def SIP.QS.SD.VALUE "3.0"
set_def SIP.QS.SD.MIN "0.0"
set_def SIP.QS.SD.MAX "10.0"
set_def SIP.QS.LINE_WIDTH 0
set_def SIP.QS.COLOUR "#228b22"; #forestgreen
#align sequences
set_def SIP.ALIGN.MATCH.NAME "score for match"
set_def SIP.ALIGN.MATCH.VALUE 4
set_def SIP.ALIGN.MATCH.MIN -100
set_def SIP.ALIGN.MATCH.MAX 100
set_def SIP.ALIGN.MISMATCH.NAME "score for mis-match"
set_def SIP.ALIGN.MISMATCH.VALUE -2
set_def SIP.ALIGN.MISMATCH.MIN -100
set_def SIP.ALIGN.MISMATCH.MAX 100
set_def SIP.ALIGN.START_GAP.NAME "penalty for starting gap"
set_def SIP.ALIGN.START_GAP.DNA.VALUE 8
set_def SIP.ALIGN.START_GAP.PROTEIN.VALUE 10
set_def SIP.ALIGN.START_GAP.MIN 0
set_def SIP.ALIGN.START_GAP.MAX 100
set_def SIP.ALIGN.CONT_GAP.NAME "penalty for each residue in gap"
set_def SIP.ALIGN.CONT_GAP.DNA.VALUE 1
set_def SIP.ALIGN.CONT_GAP.PROTEIN.VALUE 10
set_def SIP.ALIGN.CONT_GAP.MIN 0
set_def SIP.ALIGN.CONT_GAP.MAX 100
set_def SIP.ALIGN.LINE_WIDTH 0
set_def SIP.ALIGN.COLOUR "#4b0082"; #indigo
#sim align sequences
set_def SIP.SIM.NUM_ALIGN.NAME1 "number of alignments"
set_def SIP.SIM.NUM_ALIGN.VALUE1 1
set_def SIP.SIM.NUM_ALIGN.MIN1 1
set_def SIP.SIM.NUM_ALIGN.MAX1 100
set_def SIP.SIM.NUM_ALIGN.NAME2 "alignments above score"
set_def SIP.SIM.NUM_ALIGN.DNA.VALUE2 20
set_def SIP.SIM.NUM_ALIGN.PROTEIN.VALUE2 300
set_def SIP.SIM.NUM_ALIGN.MIN2 1
set_def SIP.SIM.NUM_ALIGN.MAX2 10000
set_def SIP.SIM.MATCH.NAME "score for match"
set_def SIP.SIM.MATCH.VALUE 1
set_def SIP.SIM.MATCH.MIN -100
set_def SIP.SIM.MATCH.MAX 100
set_def SIP.SIM.TRANSITION.NAME "score for transition"
set_def SIP.SIM.TRANSITION.VALUE -1
set_def SIP.SIM.TRANSITION.MIN -100
set_def SIP.SIM.TRANSITION.MAX 100
set_def SIP.SIM.TRANSVERSION.NAME "score for transversion"
set_def SIP.SIM.TRANSVERSION.VALUE -1
set_def SIP.SIM.TRANSVERSION.MIN -100
set_def SIP.SIM.TRANSVERSION.MAX 100
set_def SIP.SIM.START_GAP.NAME "penalty for starting gap"
set_def SIP.SIM.START_GAP.DNA.VALUE 6.0
set_def SIP.SIM.START_GAP.PROTEIN.VALUE 12
set_def SIP.SIM.START_GAP.MIN 0
set_def SIP.SIM.START_GAP.MAX 100
set_def SIP.SIM.CONT_GAP.NAME "penalty for each residue in gap"
set_def SIP.SIM.CONT_GAP.DNA.VALUE 0.2
set_def SIP.SIM.CONT_GAP.PROTEIN.VALUE 4
set_def SIP.SIM.CONT_GAP.MIN 0
set_def SIP.SIM.CONT_GAP.MAX 100
set_def SIP.SIM.LINE_WIDTH 0
set_def SIP.SIM.COLOUR "#ffa500"; #orange
#score matrix
set_def SIP.SCORE.TYPE.BUTTON.1 "DNA"
set_def SIP.SCORE.TYPE.BUTTON.2 "protein"
set_def SIP.SCORE.TYPE.NAME "format"
set_def SIP.SCORE.TYPE.VALUE "2"
#removing duplicates
set_def SIP.DUP.NAME "Remove duplicate matches"
set_def SIP.DUP.VALUE 0
#rotate
set_def SIP.ROTATE.ORIGIN.NAME Origin
set_def SIP.ROTATE.ORIGIN.VALUE 1
# Set this to a Tcl list of the interpreter names of programs which Gap4 can
# communicate with using the Send To command. If they're not already running,
# it'll start one itself with the second half of the name. NB, interpreter
# names not listed here, but containing an EventHandler function will still be
# listed.
# Eg "set_def GAP_SEND_TO {{Prog1 prog1} {Prog2 {/bin/prog2 -s}}}"
set_def SIP_SEND_TO {{Nip4 nip4}}
#
# Select which plots which want to be plotted by default on top of another plot
# eg
#set_def STOPCODON GENESEARCH
# will plot stop codons on top of any gene search plot
# limitations: can't plot something of 1 frame on a plot of 3 frames
#
set_def BESTDIAGONALS ""
set_def SIMILARSPANS ""
set_def MATCHINGWORDS ""
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