source: branches/profile/SH/arb_dnapars

Last change on this file was 11626, checked in by westram, 10 years ago
  • Property svn:eol-style set to native
  • Property svn:executable set to *
  • Property svn:keywords set to Author Date Id Revision
File size: 1.7 KB
Line 
1#!/bin/bash -x
2
3if [ -z "$7" ]; then
4    echo "Usage: arb_dnapars bootstrap searchdepth viewreport randomize transversion_pars threshold_pars interactive"
5else
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
63fi
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