sub <\/span>translate<\/span> {<\/span><\/div> <\/div>
# Translate the input file from dna to protein, replacing the<\/span><\/div> # original file. Sequences that are already protein remain<\/span><\/div> # untouched.<\/span><\/div> <\/div>
my<\/span> (<\/span> $filename<\/span>,<\/span> $fullpath<\/span> )<\/span> =<\/span> @_<\/span>;<\/span><\/div> <\/div>
# Input sequence stream.<\/span><\/div> my<\/span> $seqI<\/span> =<\/span> Bio::<\/span>SeqIO<\/span>-><\/span>new<\/span>(<\/span> -<\/span>file<\/span> =><\/span> $fullpath<\/span> );<\/span><\/div> <\/div>
# Output sequence stream.<\/span><\/div> my<\/span> $tempfile<\/span> =<\/span> File::<\/span>Temp<\/span>-><\/span>new<\/span>(<\/span> SUFFIX<\/span> =><\/span> '.fasta'<\/span> )<\/span>-><\/span>filename<\/span>;<\/span><\/div> my<\/span> $seqO<\/span> =<\/span> Bio::<\/span>SeqIO<\/span>-><\/span>new<\/span>(<\/span><\/div> -<\/span>file<\/span> =><\/span> ">$tempfile"<\/span>,<\/span><\/div> -<\/span>format<\/span> =><\/span> 'fasta'<\/span><\/div> );<\/span><\/div> <\/div>
# Translate dna sequences and write to temp file.<\/span><\/div> while<\/span> (<\/span> my<\/span> $seq<\/span> =<\/span> $seqI<\/span>-><\/span>next_seq<\/span> )<\/span> {<\/span><\/div> if<\/span> (<\/span> $seq<\/span>-><\/span>alphabet<\/span> eq<\/span> 'dna'<\/span> )<\/span> {<\/span><\/div> $seq<\/span> =<\/span> $seq<\/span>-><\/span>translate<\/span>;<\/span><\/div> }<\/span><\/div> $seqO<\/span>-><\/span>write_seq<\/span>(<\/span>$seq<\/span>);<\/span><\/div> }<\/span><\/div> <\/div>
$_<\/span>-><\/span>close<\/span> for<\/span> (<\/span> $seqI<\/span>,<\/span> $seqO<\/span> );<\/span><\/div> <\/div>
# Replace the original file with the temporary one with the<\/span><\/div> # translated sequences.<\/span><\/div> move<\/span>(<\/span> $tempfile<\/span>,<\/span> $fullpath<\/span> );<\/span><\/div> <\/div>
}<\/span><\/div><\/pre><\/div>\n \n <\/div>\n\n