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lib/Bio/Tools/Run/Alignment/TCoffee.pm  view on Meta::CPAN

sub _setinput {
    my ($self,$input) = @_;
    my ($infilename, $seq, $temp, $tfh);
    #  If $input is not a reference it better be the name of a
    # file with the sequence/ alignment data...
    my $type = '';
    if (! ref $input) {
        # check that file exists or throw
        $infilename = $input;
        unless (-e $input) {return 0;}
        # let's peek and guess
        open(my $IN,$infilename) || $self->throw("Cannot open $infilename");
        my $header = <$IN>;
        if( $header =~ /^\s+\d+\s+\d+/ ||
            $header =~ /Pileup/i ||
            $header =~ /clustal/i ) { # phylip
            $type = 'A';
        }

        # On some systems, having filenames with / in them (ie. a file in a
        # directory) causes t-coffee to completely fail. It warns on all systems.

lib/Bio/Tools/Run/Alignment/TCoffee.pm  view on Meta::CPAN

 Title       : IN
 Description : (optional) input filename, this is specified when
               align so should not use this directly unless one
               understand TCoffee program very well.

=head2 TYPE

 Title       : TYPE
 Args        : [string] DNA, PROTEIN
 Description : (optional) set the sequence type, guessed automatically
               so should not use this directly

=head2 PARAMETERS

 Title       : PARAMETERS
 Description : (optional) Indicates a file containing extra parameters

=head2 EXTEND

 Title       : EXTEND