Example1:
perl -e 'while(<>) {if($_=~/^>/) {print $_;} else {$_=~tr/ATCG/TAGC/; print $_;}}'  FILE

Example2:
perl -e 'while(<>) {if($_=~/^P00520/) {print $_;}}' FILE

Example3:
perl -e '$count=0; while(<>) {$count++; if($count<=250) {print $_;}}' FILE

Example4:
perl -e '$count=0; while(<>) {if($_=~/^>/) {$count++; print ">$count\n";} else {print $_;}}' FILE

Example 5:
perl -e 'while(<>) {my $line=$_; if($line!~/^\s+/) {chomp $line; my @split_line=split(/\s+/, $_); my $wanted_pos=$#split_line-1; print "$split_line[0]\t$split_line[$wanted_pos]\n";}}' FILE 

Example6:
perl -e 'my $count_serines=0; my $count_positives=0; while(<>) {my $line=$_; $count_serines++; if($line!~/^\s+/) {chomp $line; my @split_line=split(/\s+/, $_); my $wanted_pos=$#split_line-1; if($split_line[$wanted_pos] eq "*S*") {$count_positives++;}}} print "TOTAL_SERINES: ".$count_serines."\t"."POSITIVE_PREDICTIONTS: ".$count_positives."\n";' FILE