Last change
on this file was
2713,
checked in by westram, 20 years ago
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- added info message about fixed protml crash
|
-
Property svn:eol-style set to
native
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Property svn:executable set to
*
-
Property svn:keywords set to
Author Date Id Revision
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File size:
2.0 KB
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Line | |
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1 | #!/bin/bash -x |
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2 | # renames output to 'treefile' |
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3 | |
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4 | if [ -f treefile ]; then |
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5 | rm treefile |
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6 | fi |
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7 | |
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8 | if [ -z "$5" ]; then |
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9 | arb_message "Usage: arb_protml modelflag searchflag rearrange calclengths inputfile" |
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10 | else |
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11 | MODEL=$1 |
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12 | SEARCH=$2 |
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13 | REARRANGE=$3 |
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14 | CALCLENGTH=$4 |
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15 | INFILE=$5 |
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16 | |
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17 | if [ \! -s $INFILE ]; then |
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18 | arb_message "Error: no or empty input file" |
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19 | ls -al $INFILE |
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20 | else |
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21 | FLAGS="-v $MODEL" |
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22 | if [ \! "$REARRANGE" = "0" ]; then |
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23 | if [ "$SEARCH" = "-s" ]; then |
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24 | arb_message "You have selected 'Star decomposition search' AND 'Rearrangement'.\n Original protml crashed with this parameter combination.\n We fixed protml, but we did not check the results\n - so use them with care!" |
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25 | fi |
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26 | FLAGS="$FLAGS $REARRANGE" |
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27 | fi |
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28 | |
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29 | # normal tree generation with protml |
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30 | echo >arb_read_tree_args |
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31 | if [ "$SEARCH" = "-s" ]; then |
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32 | if [ "$CALCLENGTH" = "0" ]; then |
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33 | arb_message "Note: Star decomposition search always calculates branchlengths" |
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34 | fi |
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35 | # Star decomposition search (may not be the ML tree) |
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36 | protml $FLAGS -I -s $INFILE |
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37 | else |
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38 | # Exhaustive search or quickadd |
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39 | protml $FLAGS -I $SEARCH $INFILE | tail -1 >outtree # write last tree to outtree |
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40 | |
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41 | if [ -s outtree ]; then |
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42 | if [ "$CALCLENGTH" = "1" ]; then |
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43 | echo "1" >intree #no of trees |
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44 | cat outtree >>intree |
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45 | protml -v $MODEL -u -I $INFILE intree # calculates branch lengths |
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46 | else |
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47 | mv outtree protml.tre |
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48 | fi |
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49 | else |
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50 | arb_message "Error running protml: outtree is empty" |
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51 | fi |
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52 | fi |
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53 | |
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54 | if [ \! -s protml.tre ]; then |
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55 | arb_message "Error running protml: protml.tre was not generated or is empty" |
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56 | else |
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57 | mv protml.tre treefile |
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58 | fi |
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59 | fi |
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60 | |
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61 | # remove protml junk: |
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62 | rm protml.eps protml.tpl |
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63 | fi |
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64 | |
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