/usr/share/staden/etc/cap3rc 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 | load_package %L/cap3 {} cap3 0
set_menu gap_menu
add_menu Assembly 1 2 left
set fs ""
catch {set fs [open "|cap3_s" r]}
if {$fs == ""} {
add_cascade {Assembly.CAP3 Assembly} 0 0
} else {
catch {close $fs}
add_cascade {Assembly.CAP3 Assembly} 12 22
}
add_command {Assembly.CAP3 Assembly.Perform CAP3 assembly} \
12 22 {HuangAssembly_3 \$io 1}
add_command {Assembly.CAP3 Assembly.Import CAP3 assembly data} \
12 22 {HuangImport_3 \$io}
add_command {Assembly.CAP3 Assembly.Perform and import CAP3 assembly} \
12 22 {HuangAssembly_3 \$io 2}
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_f_or_l_out WHICH.NAME "Output to"
set_defx defs_f_or_l_out WHICH.BUTTONS {list file}
set_defx defs_f_or_l_out WHICH.VALUE 2
set_defx defs_f_or_l_out NAME.NAME "List or file name"
set_defx defs_f_or_l_out NAME.BROWSE "Browse"
set_defx defs_f_or_l_out NAME.VALUE ""
set_def HUANG_ASSEMBLY1.WIN .cap3_perform_assembly
set_def HUANG_ASSEMBLY2.WIN .cap3_import_assembly
set_def HUANG_ASSEMBLY3.WIN .cap3_perform_import_assembly
set_def HUANG_ASSEMBLY.INFILE $defs_f_or_l_in
set_def HUANG_ASSEMBLY.INFILE.WHICH.NAME "Input readings from"
set_def HUANG_ASSEMBLY.CONS.NAME "Use constraint file"
set_def HUANG_ASSEMBLY.CONS.VALUE 0
set_def HUANG_ASSEMBLY.DEST.NAME "Destination directory"
set_def HUANG_ASSEMBLY.DEST.VALUE "assemble"
set_def HUANG_ASSEMBLY.FORMAT.NAME "Input reading format"
set_def HUANG_ASSEMBLY.FORMAT.VALUE 1
set_def HUANG_ASSEMBLY.FORMAT.BUTTON.1 "experiment"
set_def HUANG_ASSEMBLY.FORMAT.BUTTON.2 "fasta"
set_def HUANG_ASSEMBLY.OUTFILE $defs_f_or_l_out
set_def HUANG_ASSEMBLY.OUTFILE.WHICH.NAME "Save failures to"
set_def HUANG_ASSEMBLY.INDIR.NAME "Directory containing assembled readings"
set_def HUANG_ASSEMBLY.FOFN "fofn"
set_def HUANG_ASSEMBLY.BAND_EXP.NAME "Band expansion size"
set_def HUANG_ASSEMBLY.BAND_EXP.VALUE 20
set_def HUANG_ASSEMBLY.BAND_EXP.MIN 10
set_def HUANG_ASSEMBLY.QUAL_DIFF.NAME "Base quality cutoff for differences"
set_def HUANG_ASSEMBLY.QUAL_DIFF.VALUE 20
set_def HUANG_ASSEMBLY.QUAL_DIFF.MIN 16
set_def HUANG_ASSEMBLY.QUAL_DIFF.MAX 99
set_def HUANG_ASSEMBLY.QUAL_CLIP.NAME "Base quality cutoff for clipping"
set_def HUANG_ASSEMBLY.QUAL_CLIP.VALUE 10
set_def HUANG_ASSEMBLY.QUAL_CLIP.MIN 6
set_def HUANG_ASSEMBLY.QUAL_CLIP.MAX 99
set_def HUANG_ASSEMBLY.QSCORE.NAME "Max qscore sum at differences"
set_def HUANG_ASSEMBLY.QSCORE.VALUE 200
set_def HUANG_ASSEMBLY.QSCORE.MIN 100
set_def HUANG_ASSEMBLY.CLEARANCE.NAME "Clearance between no. of diff"
set_def HUANG_ASSEMBLY.CLEARANCE.VALUE 30
set_def HUANG_ASSEMBLY.CLEARANCE.MIN 10
set_def HUANG_ASSEMBLY.GAP_PENALTY.NAME "Gap penalty factor"
set_def HUANG_ASSEMBLY.GAP_PENALTY.VALUE 6
set_def HUANG_ASSEMBLY.GAP_PENALTY.MIN 0
set_def HUANG_ASSEMBLY.MATCH_SCORE.NAME "Match score factor"
set_def HUANG_ASSEMBLY.MATCH_SCORE.VALUE 2
set_def HUANG_ASSEMBLY.MATCH_SCORE.MIN 0
set_def HUANG_ASSEMBLY.MISMATCH_SCORE.NAME "Mismatch score factor"
set_def HUANG_ASSEMBLY.MISMATCH_SCORE.VALUE -5
set_def HUANG_ASSEMBLY.MISMATCH_SCORE.MAX 0
set_def HUANG_ASSEMBLY.OVERLAP_LENGTH.NAME "Overlap length cutoff"
set_def HUANG_ASSEMBLY.OVERLAP_LENGTH.VALUE 30
set_def HUANG_ASSEMBLY.OVERLAP_LENGTH.MIN 20
set_def HUANG_ASSEMBLY.OVERLAP_IDENTITY.NAME "Overlap percent identity cutoff"
set_def HUANG_ASSEMBLY.OVERLAP_IDENTITY.VALUE 75
set_def HUANG_ASSEMBLY.OVERLAP_IDENTITY.MIN 65
set_def HUANG_ASSEMBLY.OVERLAP_SIMILARITY.NAME "Overlap similarity score cutoff"
set_def HUANG_ASSEMBLY.OVERLAP_SIMILARITY.VALUE 500
set_def HUANG_ASSEMBLY.OVERLAP_SIMILARITY.MIN 100
set_def HUANG_ASSEMBLY.MIN_CORRECTION.NAME "Min number of constraints for correction"
set_def HUANG_ASSEMBLY.MIN_CORRECTION.VALUE 4
set_def HUANG_ASSEMBLY.MIN_CORRECTION.MIN 0
set_def HUANG_ASSEMBLY.MIN_LINKING.NAME "Min number of constraints for linking"
set_def HUANG_ASSEMBLY.MIN_LINKING.VALUE 2
set_def HUANG_ASSEMBLY.MIN_LINKING.MIN 0
set_def HUANG_ASSEMBLY.PREFIX.NAME "Prefix string for output file names"
set_def HUANG_ASSEMBLY.PREFIX.VALUE cap
|