UNIX for Dummies Questions & Answers

grep ">" inputfile > Outputfile

grep "[[:alpha:]]\{10\}" inputfile > outputfile

$ perl -nle 'if ($a == 0) { push @x, $_; $a=1; next; }
             if ($a == 1 && length($_) >=11 && length($_) <= 17)
             { print @x; print $_; $a=0; @x=(); }
             else { $a=0; @x=(); }' fasta-file

$ cat fasta
> Seq 1
ACGACTAGACGATAGACGATAGA
> Seq 2
ACGATGACGTAGCAGT
> Seq 3
ACGATGACGTAGCAGT
> Seq 4
ACGATGACGTAGCAGT
> Seq 5
ACGATACGAT
> Seq 6
ASDFASKFALKJSDFKJASLDFJL
> Seq 7
ASDFASDFASDF
> Seq 8
ASAFJASDFASDFF
> Seq 9
ASDFAS
> Seq 10
ASAFJASDFASDFF
> Seq 11
ACGATGACGTAGCAGT

$ perl -nle 'if ($a == 0) { push @x, $_; $a=1; next; }
             if ($a == 1 && length($_) >=11 && length($_) <= 17)
             { push @x, ",$_"; print @x; $a=0; @x=(); }
             else { $a=0; @x=(); }' fasta | cut -c7- | sort -t, -k2 -k1n |\
  perl -F, -lane 'if ($a == 0) { push @x, @F; $a=1; $c=1; next; }
                  if ($a == 1 && $F[1] eq $x[1]) { ++$c; }
                  else { push @x, $c; print "> Seq $x[0]", " / freq $x[2]\n", $x[1]; @x=(); push @x, @F; $a=1; $c=1; }
                  END { push @x, $c; print "> Seq $x[0]", " / freq $x[2]\n", $x[1]; }'
> Seq 2 / freq 4
ACGATGACGTAGCAGT
> Seq 8 / freq 2
ASAFJASDFASDFF
> Seq 7 / freq 1
ASDFASDFASDF
$