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1 #! /bin/sh
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2
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3 # Sort MAF-format alignments by sequence name, then strand, then start
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4 # position, then end position, of the top sequence. Also, merge
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5 # identical alignments. Comment lines starting with "#" are written
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6 # at the top, in unchanged order. If option "-d" is specified, then
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7 # alignments that appear only once are omitted (like uniq -d).
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8
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9 # Minor flaws, that do not matter for typical MAF input:
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10 # 1) It might not work if the input includes TABs.
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11 # 2) Preceding whitespace is considered part of the sequence name. I
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12 # want to use sort -b, but it seems to be broken in different ways for
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13 # different versions of sort!
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14 # 3) Alignments with differences in whitespace are considered
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15 # non-identical.
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16
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17 # This script uses perl instead of specialized commands like uniq.
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18 # The reason is that, on some systems (e.g. Mac OS X), uniq doesn't
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19 # work with long lines.
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20
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21 # Make "sort" use a standard ordering:
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22 LC_ALL=C
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23 export LC_ALL
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24
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25 uniqOpt=1
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26 whichSequence=1
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27 while getopts hdn: opt
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28 do
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29 case $opt in
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30 h) cat <<EOF
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31 Usage: $(basename $0) [options] my-alignments.maf
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32
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33 Options:
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34 -h show this help message and exit
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35 -d only print duplicate alignments
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36 -n sort by the n-th sequence (default: 1)
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37 EOF
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38 exit
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39 ;;
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40 d) uniqOpt=2
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41 ;;
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42 n) whichSequence="$OPTARG"
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43 ;;
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44 esac
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45 done
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46 shift $((OPTIND - 1))
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47
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48 baseField=$((6 * $whichSequence))
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49 a=$(($baseField - 4))
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50 a=$a,$a
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51 b=$(($baseField - 1))
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52 b=$b,$b
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53 c=$(($baseField - 3))
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54 c=$c,$c
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55 d=$(($baseField - 2))
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56 d=$d,$d
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57
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58 # 1) Add digits to "#" lines, so that sorting won't change their order.
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59 # 2) Replace spaces, except in "s" lines.
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60 # 3) Join each alignment into one big line.
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61 perl -pe '
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62 s/^#/sprintf("#%.9d",$c++)/e;
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63 y/ /\a/ unless /^s/;
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64 y/\n/\b/ if /^\w/;
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65 ' "$@" |
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66
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67 sort -k$a -k$b -k${c}n -k${d}n | # sort the lines
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68
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69 # Print only the first (or second) of each run of identical lines:
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70 perl -ne '$c = 0 if $x ne $_; $x = $_; print if ++$c == '$uniqOpt |
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71
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72 # 1) Remove the digits from "#" lines.
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73 # 2) Restore spaces and newlines.
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74 perl -pe '
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75 s/^#.{9}/#/;
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76 y/\a\b/ \n/;
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77 '
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