gistfile1.sh

$ cat test.txt
MPLE	MIR	ABUNDANCE
sample1	mir1	30
sample1	mir3	100
sample1	mir4	120
sample2	mir1	40
sample2	mir2	200
sample3	mir1	190
sample3 mir1    400
sample4 mir4    20
sample5 mir1    19

$ perl -ane 'if ($. > 1){$r{$F[0].":".$F[1]}=$F[2];unless($F[0]~~@s){push @s,$F[0];}unless($F[1]~~@m){push @m,$F[1];}}END{print "Samples\t".join("\t",@s)."\n";for($i=0;$i<@m;$i++){print $m[$i];for($j=0;$j<@s;$j++){(not defined $r{$s[$j].":".$m[$i]})?print "\t".0:print"\t".$r{$s[$j].":".$m[$i]};}print "\n";}}' test.txt
Samples	sample1	sample2	sample3	sample4	sample5
mir1	30	40	400	0	19
mir3	100	0	0	0	0
mir4	120	0	0	20	0
mir2	0	200	0	0	0