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bin/abbr-ids-fas.pl  view on Meta::CPAN

my $prefix_mapper;
if ($ARGV_id_prefix_mapper) {
    ### Taking prefixes from: $ARGV_id_prefix_mapper
    $prefix_mapper = IdMapper->load($ARGV_id_prefix_mapper);
}

for my $infile (@ARGV_infiles) {

    ### Processing: $infile
    my $ali = Ali->load($infile);
    $ali->dont_guess;

    # determine seq_id prefix
    my $prefix = $ARGV_id_prefix // q{};        # defaults to no prefix
    if ($prefix_mapper) {                       # infile paths are ignored
        my ($filename) = fileparse($infile);
        $prefix .= $prefix_mapper->abbr_id_for($filename);
    }
    if ($prefix) {
        ### Prefixing seq ids with: $prefix
        $prefix .= '|';                         # add '|' separator

bin/extract-mcl-out.pl  view on Meta::CPAN

        next LINE if $line =~ $EMPTY_LINE
                  || $line =~ $COMMENT_LINE;

        # extract id list for current group
        my ($group, @ids) = split /\s+/xms, $line;
        $group =~ s/:\z//xms;           # remove trailing colon (:)
        my $list = IdList->new( ids => \@ids );

        # assemble Ali and store it as FASTA file
        my $ali = $list->reordered_ali($db);
        $ali->dont_guess;
        my $outfile = file($dir, change_suffix($group, '.fasta') )->stringify;
        $ali->store_fasta($outfile);
    }
}

__END__

=pod

=head1 NAME