source:
branches/stable/SH/arb_dnapars
Last change on this file was 11626, checked in by westram, 11 years ago | |
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File size: 1.7 KB |
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1 | #!/bin/bash -x |
2 | |
3 | if [ -z "$7" ]; then |
4 | echo "Usage: arb_dnapars bootstrap searchdepth viewreport randomize transversion_pars threshold_pars interactive" |
5 | else |
6 | BOOTSTRAP=$1 |
7 | SEARCH=$2 |
8 | REPORT=$3 |
9 | RANDOMIZE=$4 |
10 | TRANSVERSION_PARS=$5 |
11 | THRESHOLD_PARS=$6 |
12 | INTERACTIVE=$7 |
13 | |
14 | FLAGS= |
15 | |
16 | if [ "$RANDOMIZE" = "1" ]; then |
17 | RANDOMSEED=$(($RANDOM|1)) # a odd number |
18 | FLAGS="$FLAGS j $RANDOMSEED 1" |
19 | fi |
20 | |
21 | if [ "$TRANSVERSION_PARS" = "1" ]; then |
22 | FLAGS="$FLAGS n" |
23 | fi |
24 | |
25 | if [ \! "$THRESHOLD_PARS" = "0" ]; then |
26 | FLAGS="$FLAGS t $THRESHOLD_PARS" |
27 | fi |
28 | |
29 | case $SEARCH in |
30 | 0) FLAGS="$FLAGS" ;; |
31 | 1) FLAGS="$FLAGS s n" ;; |
32 | 2) FLAGS="$FLAGS s y" ;; |
33 | *) arb_message "Illegal value for 'searchdepth'"; exit 1 ;; |
34 | esac |
35 | |
36 | if [ "$BOOTSTRAP" = "0" ]; then |
37 | if [ "$INTERACTIVE" = "0" ]; then |
38 | arb_echo $FLAGS y | dnapars |
39 | else |
40 | (arb_echo $FLAGS; cat -) | ( dnapars ; echo "Press RETURN to continue.." ) |
41 | fi |
42 | echo '' >arb_read_tree_args |
43 | arb_message "Please note: Branchlengths generated by DNAPARS have strange scaling (somehow relative to sequence length?)\n" |
44 | WHAT=dnapars |
45 | else |
46 | arb_bootstrap $BOOTSTRAP dnapars $FLAGS |
47 | WHAT=arb_bootstrap/dnapars/consense |
48 | fi |
49 | |
50 | if [ -f outfile ]; then |
51 | if [ -s outfile ]; then |
52 | if [ "$REPORT" = "1" ]; then |
53 | arb_textedit outfile & |
54 | fi |
55 | else |
56 | arb_message "$WHAT: Error: generated 'outfile' is empty" |
57 | false |
58 | fi |
59 | else |
60 | arb_message "$WHAT: Error: 'outfile' has not been generated" |
61 | false |
62 | fi |
63 | fi |
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