BioPerl-Run

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

=cut

sub _setinput {
    my ($self,$input) = @_;
    my ($infilename, $seq, $temp, $tfh);
    if (! ref $input) {
	# check that file exists or throw
	$infilename = $input;
	unless (-e $input) {return 0;}
	# let's peek and guess
	open(IN,$infilename) || $self->throw("Cannot open $infilename");
	my $header;
	while( defined ($header = <IN>) ) {
	    last if $header !~ /^\s+$/;
	}
	close(IN);
	if ( $header !~ /^>\s*\S+/ ){
	    $self->throw("Need to provide a FASTA format file to amap!");
	} 
	return ($infilename);

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

=cut

sub _setinput {
    my ($self,$input) = @_;
    my ($infilename, $seq, $temp, $tfh);
    if (! ref $input) {
	# check that file exists or throw
	$infilename = $input;
	unless (-e $input) {return 0;}
	# let's peek and guess
	open(IN,$infilename) || $self->throw("Cannot open $infilename");
	my $header;
	while( defined ($header = <IN>) ) {
	    last if $header !~ /^\s+$/;
	}
	close(IN);
	if ( $header !~ /^>\s*\S+/ ){
	    $self->throw("Need to provide a FASTA format file to kalign!");
	} 
	return ($infilename);

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

=cut

sub _setinput {
    my( $self,$input ) = @_;
    my( $infilename,$outtemp,$tfh,@sequences );
    if (! ref $input) {
        # check that file exists or throw
        return unless (-s $input && -r $input);
        # let's peek and guess
        $infilename = $input;
        open(IN,$input) || $self->throw("Cannot open $input");
        my $header;
        while( defined ($header = <IN>) ) {
            last if $header !~ /^\s+$/;  }
        close(IN);
        $header =~ /^>\s*\S+/ ||
        $self->throw("Need to provide a FASTA-formatted file to msaprobs!");
	    my $inseqio = Bio::SeqIO->new(
	        -file   => $input,

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

        $self->throw("profile does not work for this version of muscle\n");
    }
    my $infilename;
    if ( defined $alnfilename ) {
        if ( !ref $alnfilename ) {

            # check that file exists or throw
            $infilename = $alnfilename;
            unless ( -e $infilename ) { return 0; }

            # let's peek and guess
            open( IN, $infilename ) || $self->throw("Cannot open $infilename");
            my $header;
            while ( defined( $header = <IN> ) ) {
                last if $header !~ /^\s+$/;
            }
            close(IN);
            if ( $header !~ /^>\s*\S+/ ) {
                $self->throw(
                    "Need to provide a FASTA format file to muscle profile!");
            }

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

        $self->throw(
            "Bad input data or less than 2 sequences in $infilename !");
    }
    if ( defined $seqsfilename ) {
        if ( !ref $seqsfilename ) {

            # check that file exists or throw
            $infilename = $seqsfilename;
            unless ( -e $infilename ) { return 0; }

            # let's peek and guess
            open( IN, $infilename ) || $self->throw("Cannot open $infilename");
            my $header;
            while ( defined( $header = <IN> ) ) {
                last if $header !~ /^\s+$/;
            }
            close(IN);
            if ( $header !~ /^>\s*\S+/ ) {
                $self->throw(
                    "Need to provide a FASTA format file to muscle profile!");
            }

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

sub _setinput {
    my ( $self, $input ) = @_;
    my ( $infilename, $seq, $temp, $tfh );
    if ( !ref $input ) {

        # check that file exists or throw
        $infilename = $input;
        unless ( -e $input ) { return 0; }

        # let's peek and guess
        open( IN, $infilename ) || $self->throw("Cannot open $infilename");
        my $header;
        while ( defined( $header = <IN> ) ) {
            last if $header !~ /^\s+$/;
        }
        close(IN);
        if ( $header !~ /^>\s*\S+/ ) {
            $self->throw("Need to provide a FASTA format file to muscle!");
        }
        return ($infilename);

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

=cut

sub _setinput {
    my ($self,$input) = @_;
    my ($infilename, $seq, $temp, $tfh);
    if (! ref $input) {
	# check that file exists or throw
	$infilename = $input;
	unless (-e $input) {return 0;}
	# let's peek and guess
	open(IN,$infilename) || $self->throw("Cannot open $infilename");
	my $header;
	while( defined ($header = <IN>) ) {
	    last if $header !~ /^\s+$/;
	}
	close(IN);
	if ( $header !~ /^>\s*\S+/ ){
	    $self->throw("Need to provide a FASTA format file to probalign!");
	} 
	return ($infilename);

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

=cut

sub _setinput {
    my ($self,$input) = @_;
    my ($infilename, $seq, $temp, $tfh);
    if (! ref $input) {
	# check that file exists or throw
	$infilename = $input;
	unless (-e $input) {return 0;}
	# let's peek and guess
	open(IN,$infilename) || $self->throw("Cannot open $infilename");
	my $header;
	while( defined ($header = <IN>) ) {
	    last if $header !~ /^\s+$/;
	}
	close(IN);
	if ( $header !~ /^>\s*\S+/ ){
	    $self->throw("Need to provide a FASTA format file to probcons!");
	} 
	return ($infilename);

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

=cut

sub _setinput {
    my ($self,$input) = @_;
    my ($infilename, $seq, $temp, $tfh);
    if (! ref $input) {
	# check that file exists or throw
	$infilename = $input;
	unless (-e $input) {return 0;}
	# let's peek and guess
	open(IN,$infilename) || $self->throw("Cannot open $infilename");
	my $header;
	while( defined ($header = <IN>) ) {
	    last if $header !~ /^\s+$/;
	}
	close(IN);
	if ( $header !~ /^>\s*\S+/ ){
	    $self->throw("Need to provide a FASTA format file to proda!");
	} 
	return ($infilename);

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

	} else {
		$self->throw("Must provide named filespec");
	}
	
	for (keys %args) {
		m/bam/ && do {
			return 'bam';
		};
		do {
			return unless ( -e $args{$_} && -r _ );
			my $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$args{$_});
			return $guesser->guess if grep {$guesser->guess =~ m/$_/} @{$accepted_types{$_}};
		}
	}
	return;
}

=head2 version()

 Title   : version
 Usage   : $version = $bedtools_fac->version()
 Function: Returns the program version (if available)

lib/Bio/Tools/Run/Primer3.pm  view on Meta::CPAN

#
# Copyright (c) 1997-2001 bioperl, Chad Matsalla. All Rights Reserved.
#           This module is free software; you can redistribute it and/or
#           modify it under the same terms as Perl itself. 
#
# Copyright Chad Matsalla
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
#
# But I have modified lots of it, so I guess I should add:
#
# Copyright (c) 2003 bioperl, Rob Edwards. All Rights Reserved.
#           This module is free software; you can redistribute it and/or
#           modify it under the same terms as Perl itself. 
#
# Copyright Rob Edwards
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code

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

=cut

sub _fastize {
    my $self = shift;
    my $data = shift;
    for ($data) {
	!ref && do {
	    # suppose a fasta file name
	    $self->throw('Sequence file not found') unless -e $data;
	    my $guesser = Bio::Tools::GuessSeqFormat->new(-file => $data);
	    $self->throw('Sequence file not in FASTA format') unless
		$guesser->guess eq 'fasta';
	    last;
	};
	(ref eq 'ARRAY') && (ref $$data[0]) &&
	    ($$data[0]->isa('Bio::Seq') || $$data[0]->isa('Bio::PrimarySeq'))
	    && do {
		my $fh = File::Temp->new(TEMPLATE => 'DBDXXXXX', 
					 UNLINK => 0, 
					 DIR => $self->db_dir,
					 SUFFIX => '.fas');
		my $fname = $fh->filename;

t/BEDTools.t  view on Meta::CPAN

            is( $lines, $result_lookup{$command}, " - number of lines");
        } elsif ($command eq 'genome_coverage') {
            $v && diag(" check result file is correct size");
            ok eval { (-e $file)&&(-r _) }, "make readable output";
            open (FILE, $file);
            my $lines =()= <FILE>;
            close FILE;
            is( $lines, $result_lookup{$command}, " - number of lines");
        } else {
            $v && diag(" check can get internal result format matches result file");
            my $guesser = Bio::Tools::GuessSeqFormat->new( -file => $file );
            for ($format_lookup{$command}) {
                m/^(?:bed|bedpe|tab)$/ && do {
                    is( $guesser->guess, 'tab', "file format of '$file' consistent with claim for '$command'" );
                    last;
                };
                m/^fasta$/ && do {
                    is( $guesser->guess, 'fasta', "file format consistent with claim for '$command'" );
                }
            }
        }
        $v && diag(" check can get and set wanted result type");
        is( $bedtoolsfac->want('Bio::Root::IO'), 'Bio::Root::IO',
            "can set want to IO object for command '$command'" );
        $v && diag(" check can get a Bio::Root::IO object");
        ok( my $objres = $bedtoolsfac->result, "can get the basic object result for command '$command'" );
        $v && diag(" - check can it is actually a Bio::Root::IO object");
        isa_ok( $objres, 'Bio::Root::IO', "returned object is correct for command '$command'" );

t/MSAProbs.t  view on Meta::CPAN

	$factory = Bio::Tools::Run::Alignment::MSAProbs->new(@params);
	my @methods = qw(quiet verbose outfile iterations clustalw consistency
	                 alignment_order annot_file version num_threads);
	can_ok($factory, @methods);
	is($factory->annot_file, $annotfile,'annotation file');
	$aln = $factory->align($seq_array_ref);
	is $aln->num_sequences, 7;
	$s1_perid = POSIX::ceil($aln->average_percentage_identity);
	is($s1_perid == 43, 1 );
	
	my $guesser = Bio::Tools::GuessSeqFormat->new(-file => $outfile);
	my $type = $guesser->guess;
	is($type, 'clustalw', "Expected output is clustalw formatted");
	$inputfilename = test_input_file("cysprot1a.fa");
	$aln = $factory->align($inputfilename);
	is $aln->num_sequences, 3;
	$s1_perid = POSIX::ceil($aln->average_percentage_identity);
	
	is($s1_perid == 42, 1 );
}