Bio-App-SELEX-RNAmotifAnalysis

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bin/RNAmotifAnalysis  view on Meta::CPAN

my $TRUE         = 1;
my $FALSE        = 0;
my $SPACE        = q{ };
my $EMPTY_STRING = q{};
my $VERBOSE      = 1;

my $FASTQ_TYPE  = 'fastq';
my $SIMPLE_TYPE = 'simple';

# Act like a script if called as one
unless ( caller() ) { main(); }

sub main {

    my $max_clusters    = 10;
    my $num_cpus        = 5;
    my $max_distance    = 5;
    my $max_top_seqs    = 300;
    my $config_filename = $DEFAULT_CONFIG;
    my $options         = GetOptions(

bin/selex_clustal2stockholm.pl  view on Meta::CPAN

use autodie;

use lib 'lib';
use Bio::App::SELEX::Stockholm;

my $usage = "\nUsage: $0 <ClustalW file> [gc_file]
           Converts a ClustalW file (from file or STDIN) to Stockholm format.
           Only converts sequence information, unless a secondary structure
           file is given as the second argument.\n";

main(@ARGV) unless caller();

sub main {
    my @cmd_line_args = @_;
    my @argv;
    my $gc_string;
    if (@ARGV) {
        my $arg     = shift @cmd_line_args;
        my $gc_file = shift @cmd_line_args;
        if ( defined $gc_file ) {
            open( my $gc_fh, '<', $gc_file );

bin/selex_covarianceSearch  view on Meta::CPAN

my @REQUIRED_FLAGS = qw( cm fasta sto );

# CONSTANTS
#=============================================================================

#=============================================================================
# COMMAND LINE

# Run as a command-line program if not used as a module
main(@ARGV) if !caller();

sub main {

    #-------------------------------------------------------------------------
    # COMMAND LINE INTERFACE                                                 #
    #                                                                        #
    my ( $opt, $usage ) = describe_options(
        '%c %o <some-arg>',
        [ 'cm=s',     'file name for the input covariance model (required)', ],
        [ 'fasta=s',  'file name for the FASTA file (required)',             ],

lib/Bio/App/SELEX/RNAmotifAnalysis.pm  view on Meta::CPAN

my $TRUE         = 1;
my $FALSE        = 0;
my $SPACE        = q{ };
my $EMPTY_STRING = q{};
my $VERBOSE      = 1;

my $FASTQ_TYPE  = 'fastq';
my $SIMPLE_TYPE = 'simple';

# Act like a script if called as one
unless ( caller() ) { main(); }

sub main {

    my $max_clusters    = 10;
    my $num_cpus        = 5;
    my $max_distance    = 5;
    my $max_top_seqs    = 300;
    my $config_filename = $DEFAULT_CONFIG;
    my $options         = GetOptions(

lib/Bio/App/SELEX/selex_clustal2stockholm.pl  view on Meta::CPAN

use autodie;

use lib 'lib';
use Bio::App::SELEX::Stockholm;

my $usage = "\nUsage: $0 <ClustalW file> [gc_file]
           Converts a ClustalW file (from file or STDIN) to Stockholm format.
           Only converts sequence information, unless a secondary structure
           file is given as the second argument.\n";

main(@ARGV) unless caller();

sub main {
    my @cmd_line_args = @_;
    my @argv;
    my $gc_string;
    if (@ARGV) {
        my $arg     = shift @cmd_line_args;
        my $gc_file = shift @cmd_line_args;
        if ( defined $gc_file ) {
            open( my $gc_fh, '<', $gc_file );

lib/Bio/App/SELEX/selex_covarianceSearch  view on Meta::CPAN

my @REQUIRED_FLAGS = qw( cm fasta sto );

# CONSTANTS
#=============================================================================

#=============================================================================
# COMMAND LINE

# Run as a command-line program if not used as a module
main(@ARGV) if !caller();

sub main {

    #-------------------------------------------------------------------------
    # COMMAND LINE INTERFACE                                                 #
    #                                                                        #
    my ( $opt, $usage ) = describe_options(
        '%c %o <some-arg>',
        [ 'cm=s',     'file name for the input covariance model (required)', ],
        [ 'fasta=s',  'file name for the FASTA file (required)',             ],