Shell Programming and Scripting

awk '!a[$1]{a[$1]=$2;b[$1]=$3 FS $4} $2<a[$1]{a[$1]=$2} END{for(i in a)print i, a[i], b[i]}' file

myFile="TestFile.txt"
cut -f1 -d" " "${myFile}" | sort | uniq | \
while read fKey
do
	egrep '^'"${fKey}"'' "${myFile}" | sort -n -k2 | head -1
done

$ cut -f1 -d" " "${myFile}" | sort | uniq | while read fKey; do egrep '^'"${fKey}"'' "${myFile}" | sort -n -k2 | head -1; done
AAAAAAAAAC      46      AA636074        _
AAAAAAAAAC      46      _       Hs.621716
AAAAAAAAAC      77      AI861786        _
AAAAAAAAAC      77      BE536886        _
AAAAAAAAAC      77      BE548727        _
AAAAAAAAAC      77      BF691443        _
AAAAAAAAAC      79      BF754052        _
AAAAAAAAAC      80      BI004369        _
AAAAAAAAAC      86      BU535655        _
AAAAAAAAAC      86      BU539770        _
AAAAAAAAAC      86      BX111054        _
AAAAAAAAAC      86      BX643752        _
AAAAAAAAAC      86      CA390277        _
AAAAAAAAAC      94      CD522477        _
AAAAAAAAAC      94      DR159089        _
AAAAAAAAAG      100     F24242  _
AAAAAAAAAG      26      _       Hs.445936
AAAAAAAAAG      46      _       Hs.567437
AAAAAAAAAG      5       _       Hs.190440

awk '!a[$1]{a[$1]=$2;b[$1]=$3 FS $4} $2<a[$1]{a[$1]=$2} END{for(i in a)print i, a[i], b[i]}' file

$
$
$ cat f15
AAAAAAAAAC 46 _ Hs.621716
AAAAAAAAAC 46 AA636074 _
AAAAAAAAAC 77 AI861786 _
AAAAAAAAAC 77 BE536886 _
AAAAAAAAAC 77 BE548727 _
AAAAAAAAAC 77 BF691443 _
AAAAAAAAAC 79 BF754052 _
AAAAAAAAAC 80 BI004369 _
AAAAAAAAAC 86 BU535655 _
AAAAAAAAAC 86 BU539770 _
AAAAAAAAAC 86 BX111054 _
AAAAAAAAAC 86 BX643752 _
AAAAAAAAAC 86 CA390277 _
AAAAAAAAAC 94 CD522477 _
AAAAAAAAAC 94 DR159089 _
AAAAAAAAAG 5 _ Hs.190440
AAAAAAAAAG 26 _ Hs.445936
AAAAAAAAAG 46 _ Hs.567437
AAAAAAAAAG 74 _ Hs.674701
AAAAAAAAAG 77 _ Hs.700965
AAAAAAAAAG 77 AI034458 _
AAAAAAAAAG 77 AV699522 _
AAAAAAAAAG 77 AV719142 _
AAAAAAAAAG 79 AW150843 _
AAAAAAAAAG 80 AW801953 _
AAAAAAAAAG 80 AW857024 _
AAAAAAAAAG 86 BC033980 Hs.721040
AAAAAAAAAG 86 BE072635 _
AAAAAAAAAG 86 BF104499 _
AAAAAAAAAG 86 BF897128 _
AAAAAAAAAG 93 BG537298 _
AAAAAAAAAG 93 BG706646 _
AAAAAAAAAG 94 BI025564 _
AAAAAAAAAG 94 BX425052 _
AAAAAAAAAG 100 F24242 _
$
$ 
$ ##
$ perl -lane 'if ($.==1) {
                $rec = $_;
                $p=$F[0];
                $m=$F[1];
              } elsif ($p eq $F[0]) {
                $rec = $_ if $F[1] < $m;
              } else {
                push @x, $rec;
                $rec = $_;
                $p=$F[0];
                $m=$F[1];
              }
              END {push @x, $rec; print for (@x)}
             ' f15
AAAAAAAAAC 46 _ Hs.621716
AAAAAAAAAG 5 _ Hs.190440
$
$