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--- ./Array.pm	2009/01/17 16:37:01	1.1
+++ ./Array.pm	2009/01/17 20:16:42
@@ -136,6 +136,18 @@
     }    
 }
 
+sub sort_in_place : method {
+   my ($attr, $reader, $writer) = @_;
+   return sub {
+      my ($instance, $predicate) = @_;

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my $protease = Bio::Protease->new(specificity => 'trypsin');

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my $cutting_pattern = Bio::Tools::SeqPattern->new(
    -SEQ => 'XXXW[^P]RSX', -TYPE => 'Amino'
);

my $protease = Bio::Protease->new(specificity => $cutting_pattern);

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my $nobel_prize_winning_specificity_model = sub {
    my $peptide = shift;
    # decide whether to cut $peptide or not
}

my $protease = Bio::Protease->new(
    specificity => $nobel_prize_winning_specificity_model;
);

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my @products = $protease->digest('MAAEEELLKKVVIKP');

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my @cut_sites = $protease->cleavage_sites($seq);

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my @products = $protease->cut($seq, $cut_sites[rand @cut_sites]);

brunoV

We couldn’t find that file to show.

brunoV

sub translate {

    # Translate the input file from dna to protein, replacing the
    # original file. Sequences that are already protein remain
    # untouched.

    my ( $filename, $fullpath ) = @_;

    # Input sequence stream.
    my $seqI = Bio::SeqIO->new( -file => $fullpath );

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sub translate {

    my ( $filename, $fullpath ) = @_;

    my $seqI = Bio::SeqIO->new( -file => $fullpath );

    my $tempfile = File::Temp->new( SUFFIX => '.fasta' )->filename;
    my $seqO     = Bio::SeqIO->new(
        -file   => ">$tempfile",
        -format => 'fasta'