Bio::Tools::Run Infernal
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Summary
Bio::Tools::Run::Infernal - Wrapper for local execution of cmalign, cmbuild,
cmsearch, cmscore
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::SearchIO
Bio::SeqIO
Data::Dumper
Inherit
Bio::ParameterBaseI Bio::Root::Root Bio::Tools::Run::WrapperBase
Synopsis
  # parameters which are switches are set with any value that evals TRUE,
  # others are set to a specific value

  my $factory = Bio::Tools::Run::Infernal->new(@params);

  # run cmalign|cmbuild|cmsearch|cmscore|cmemit directly as a wrapper method
  # this resets the program flag if previously set

  $factory->cmsearch(@seqs); # searches Bio::PrimarySeqI's based on set cov. model
                             # saves output to optional outfile_name, returns
                             # Bio::SearchIO

  # only values which are allowed for a program are set, so one can use the same
  # wrapper for the following...

  $factory->cmalign(@seqs); # aligns Bio::PrimarySeqI's to a set cov. model,
                            # --merge option allows two alignments generated
                            #     from the same CM to be merged.
                            # output to outfile_name, returns Bio::AlignIO
  $factory->cmscore();      # scores set cov. model against Bio::PrimarySeqI,
                            # output to outfile_name/STDOUT.
  $factory->cmbuild($aln); # builds covariance model based on alignment
                           # CM to outfile_name or model_file (one is required
                           # here), output to STDOUT.
  $factory->cmemit();      # emits sequence from specified cov. model;
                           # set one if no file specified. output to
                           # outfile_name, returns Bio::SeqIO or (if -a is set)
                           # Bio::AlignIO
  $factory->cmcalibrate($file); # calibrates specified cov. model; output to
                                # STDOUT
  $factory->cmstat($file); # summary stats for cov. model; set one if no file
                           # specified; output to STDOUT

  # run based on the setting of the program parameter

  my $factory = Bio::Tools::Run::Infernal->new(-program => 'cmsearch',
                                                @params);
  my $search = $factory->run($seq);

  # using cmsearch returns a Bio::SearchIO object

  while (my $result = $searchio->next_result){
   while(my $hit = $result->next_hit){
    while (my $hsp = $hit->next_hsp){
            print join("\t", ( $r->query_name,
                               $hit->name,
                               $hsp->hit->start,
                               $hsp->hit->end,
                               $hsp->meta,
                               $hsp->score,
                               )), "\n";
    }
   }
  }
Description
Wrapper module for Sean Eddy's Infernal suite of programs. The current
implementation runs cmsearch, cmcalibrate, cmalign, cmemit, cmbuild, cmscore,
and cmstat. cmsearch will return a Bio::SearchIO, cmemit a Bio::SeqIO/AlignIO,
and cmalign a Bio::AlignIO. All others send output to STDOUT. Optionally,
any program's output can be redirected to outfile_name.
We HIGHLY suggest upgrading to Infernal 1.0. In that spirit, this wrapper now
supports parameters for Infernal 1.0 only; for wrapping older versions of
Infernal we suggest using the version of Bio::Tools::Run::Infernal that came
with previous versions of BioPerl-run.
NOTE: Due to conflicts in the way Infernal parameters are now formatted vs.
subroutine naming in Perl (specifically the inclusion of hyphens) and due to the
very large number of parameters available, setting and resetting parameters via
set_parameters() and reset_parameters() is required. All valid parameters can
be set, but only ones valid for the executable set via program()/program_name()
are used for calling the executables, the others are silently ignored.
Methods
newDescriptionCode
programDescriptionCode
program_nameDescriptionCode
model_fileDescriptionCode
program_dirDescriptionCode
versionDescriptionCode
runDescriptionCode
cmsearchDescriptionCode
cmalignDescriptionCode
cmemitDescriptionCode
cmbuildDescriptionCode
cmscoreDescriptionCode
cmcalibrateDescriptionCode
cmstatDescriptionCode
set_parametersDescriptionCode
reset_parametersDescriptionCode
validate_parametersDescriptionCode
parameters_changedDescriptionCode
available_parametersDescriptionCode
get_parametersDescriptionCode
to_exe_stringDescriptionCode
_run
No description
Code
_writeSeqFileDescriptionCode
_writeAlignFileDescriptionCode
_dump_params
No description
Code
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $wrapper = Bio::Tools::Run::Infernal->new(@params)
 Function: creates a new Infernal factory
 Returns:  Bio::Tools::Run::Infernal wrapper
 Args    : list of parameters
programcodeprevnextTop
 Title   :  program
 Usage   :  $obj->program()
 Function:  Set the program called when run() is used.  Synonym of
            program_name()
 Returns :  String (program name)
 Args    :  String (program name)
 Status  :  Unstable (may delegate to program_name, which is the interface method)
program_namecodeprevnextTop
 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns:  string
 Args    : None
model_filecodeprevnextTop
 Title   :  model_file
 Usage   :  $obj->model_file()
 Function:  Set the model file used when run() is called.
 Returns :  String (file location of covariance model)
 Args    :  String (file location of covariance model)
program_dircodeprevnextTop
 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :
versioncodeprevnextTop
 Title   : version
 Usage   : $v = $prog->version();
 Function: Determine the version number of the program (uses cmsearch)
 Example :
 Returns : float or undef
 Args    : none
runcodeprevnextTop
 Title   :   run
 Usage   :   $obj->run($seqFile)
 Function:   Runs Infernal and returns Bio::SearchIO
 Returns :   A Bio::SearchIO
 Args    :   A Bio::PrimarySeqI or file name
cmsearchcodeprevnextTop
 Title   :   cmsearch
 Usage   :   $obj->cmsearch($seqFile)
 Function:   Runs Infernal cmsearch and returns Bio::SearchIO
 Returns :   A Bio::SearchIO
 Args    :   Bio::PrimarySeqI or file name
cmaligncodeprevnextTop
 Title   :   cmalign
 Usage   :   $obj->cmalign($seqFile)
 Function:   Runs Infernal cmalign and returns Bio::AlignIO
 Returns :   A Bio::AlignIO
 Args    :   Bio::PrimarySeqI or file name
cmemitcodeprevnextTop
 Title   :   cmemit
 Usage   :   $obj->cmemit($modelfile)
 Function:   Runs Infernal cmemit and returns Bio::AlignIO
 Returns :   A Bio::AlignIO
 Args    :   None; set model_file() to use a specific model
cmbuildcodeprevnextTop
 Title   :   cmbuild
 Usage   :   $obj->cmbuild($alignment)
 Function:   Runs Infernal cmbuild and saves covariance model
 Returns :   1 on success (no object for covariance models)
 Args    :   Bio::AlignIO with structural information (such as from Stockholm
             format source) or alignment file name
cmscorecodeprevnextTop
 Title   :   cmscore
 Usage   :   $obj->cmscore($seq)
 Function:   Runs Infernal cmscore and saves output
 Returns :   None
 Args    :   None; set model_file() to use a specific model
cmcalibratecodeprevnextTop
 Title   :   cmcalibrate
 Usage   :   $obj->cmcalibrate('file')
 Function:   Runs Infernal calibrate on specified CM
 Returns :   None
 Args    :   None; set model_file() to use a specific model
cmstatcodeprevnextTop
 Title   :   cmstat
 Usage   :   $obj->cmstat($seq)
 Function:   Runs Infernal cmstat and saves output
 Returns :   None
 Args    :   None; set model_file() to use a specific model
set_parameterscodeprevnextTop
 Title   : set_parameters
 Usage   : $pobj->set_parameters(%params);
 Function: sets the parameters listed in the hash or array
 Returns : None
 Args    : [optional] hash or array of parameter/values.  These can optionally
           be hash or array references
 Note    : This only sets parameters; to set methods use the method name
reset_parameterscodeprevnextTop
 Title   : reset_parameters
 Usage   : resets values
 Function: resets parameters to either undef or value in passed hash
 Returns : none
 Args    : [optional] hash of parameter-value pairs
validate_parameterscodeprevnextTop
 Title   : validate_parameters
 Usage   : $pobj->validate_parameters(1);
 Function: sets a flag indicating whether to validate parameters via
           set_parameters() or reset_parameters()
 Returns : Bool
 Args    : [optional] value evaluating to True/False
 Note    : Optionally implemented method; up to the implementation on whether
           to automatically validate parameters or optionally do so
parameters_changedcodeprevnextTop
 Title   : parameters_changed
 Usage   : if ($pobj->parameters_changed) {...}
 Function: Returns boolean true (1) if parameters have changed
 Returns : Boolean (0 or 1)
 Args    : None
 Note    : This module does not run state checks, so this always returns True
available_parameterscodeprevnextTop
 Title   : available_parameters
 Usage   : @params = $pobj->available_parameters()
 Function: Returns a list of the available parameters
 Returns : Array of parameters
 Args    : [optional] name of executable being used; defaults to returning all
           available parameters
get_parameterscodeprevnextTop
 Title   : get_parameters
 Usage   : %params = $pobj->get_parameters;
 Function: Returns list of set key-value pairs, parameter => value
 Returns : List of key-value pairs
 Args    : [optional]
           'full' - this option returns everything associated with the parameter
                    as an array ref value; that is, not just the value but also
                    the value, type, and prefix. Default is value only.
           'valid'- same a 'full', but only returns the grouping valid for the
                    currently set executable
to_exe_stringcodeprevnextTop
 Title   : to_exe_string
 Usage   : $string = $pobj->to_exe_string;
 Function: Returns string (command line string in this case)
 Returns : String 
 Args    :
_writeSeqFilecodeprevnextTop
 Title   :   _writeSeqFile
 Usage   :   obj->_writeSeqFile($seq)
 Function:   Internal(not to be used directly)
 Returns :
 Args    :
_writeAlignFilecodeprevnextTop
 Title   :   _writeAlignFile
 Usage   :   obj->_writeAlignFile($seq)
 Function:   Internal(not to be used directly)
 Returns :
 Args    :
Methods code
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    
    # these are specific parameters we do not want passed on to set_parameters
    my ($program, $model, $validate, $q, $o1, $o2) =
        $self->_rearrange([qw(PROGRAM
                           MODEL_FILE
                           VALIDATE_PARAMETERS
                           QUIET
                           OUTFILE_NAME
                           O)], @args);
    
    if ($o1 && $o2) {
        $self->warn("Only assign to either -outfile_name or -o, not both;");
    }
    my $out = $o1 || $o2;
    $self->validate_parameters($validate);
    $q          && $self->quiet($q);
    $program    && $self->program($program);
    $model      && $self->model_file($model);
    $out ||= '';
    $self->outfile_name($out);
    $self->io->_initialize_io();    
    $self->set_parameters(@args);
    return $self;
}
programdescriptionprevnextTop
sub program {
    my $self = shift;
    return $self->program_name(@_);
}
program_namedescriptionprevnextTop
sub program_name {
    my ($self) = shift;
    if (@_) {
        my $p = shift;
        $self->throw("Program '$p' not supported")
            if !exists $INFERNAL_PROGRAM{lc $p};
        $self->{'_program'} = lc $p;
        # set up cache of valid parameters
        while (my ($p, $data) = each %INFERNAL_PARAMS) {
            my %in_exe = map {$_ => 1} @$data[2..$#{$data}];
            $self->{valid_params}->{$p} = 1 if exists $in_exe{$self->{'_program'}};
        }
    }
    return $self->{'_program'};
}
model_filedescriptionprevnextTop
sub model_file {
    my $self = shift;
    return $self->{'_model_file'} = shift if @_;
    return $self->{'_model_file'};
}
program_dirdescriptionprevnextTop
sub program_dir {
    my ($self, $dir) = @_;
    if ($dir) {
        $self->{_program_dir} = $dir;
    }
    return Bio::Root::IO->catfile($ENV{INFERNALDIR}) || '';
}
versiondescriptionprevnextTop
sub version {
    my ($self) = @_;
    return unless $self->executable;
    my $exe = $self->executable;
    my $string = `$exe -h 2>&1`;
    my $v;
    if ($string =~ m{Infernal\s([\d.]+)}) {
        $v = $1;
        $self->deprecated(-message => "Only Infernal 1.0 and above is supported.",
                          -version => 1.006001) if $v < 1;
    }
    return $self->{'_progversion'} = $v || undef;
}
rundescriptionprevnextTop
sub run {
    my ($self,@seq) = @_;
    if  (ref $seq[0] && $seq[0]->isa("Bio::PrimarySeqI") ){# it is an object
        my $infile1 = $self->_writeSeqFile(@seq);
        return $self->_run($infile1);
    } elsif (ref $seq[0] && $seq[0]->isa("Bio::Align::AlignI") ){ # it is an object
        my $infile1 = $self->_writeAlignFile(@seq);
        return $self->_run($infile1);
    } else {
        return $self->_run(@seq);
    }
}
cmsearchdescriptionprevnextTop
sub cmsearch {
    my ($self,@seq) = @_;
    $self->program('cmsearch');
    if  (ref $seq[0] && $seq[0]->isa("Bio::PrimarySeqI") ){# it is an object
        my $infile1 = $self->_writeSeqFile(@seq);
        return  $self->_run(-seq_files => [$infile1]);
    } else {
        return  $self->_run(-seq_files =>\@ seq);
    }
}
cmaligndescriptionprevnextTop
sub cmalign {
    my ($self,@seq) = @_;
    $self->program('cmalign');
    if (ref $seq[0]) { # it is an object
        if ($seq[0]->isa("Bio::PrimarySeqI") ){
            my $infile1 = $self->_writeSeqFile(@seq);
            return  $self->_run(-seq_files => [$infile1]);
        } elsif ( $seq[0]->isa("Bio::Align::AlignI") ) {
            if (scalar(@seq) != 2) {
                $self->throw("")
            }
            my $infile1 = $self->_writeAlignFile($seq[0]);
            my $infile2 = $self->_writeAlignFile($seq[1]);
            return  $self->_run(-align_files => [$infile1, $infile2]);
        }
    } else {
        # we can maybe add a check for the file extension and try to DTRT
        my %params = $self->get_parameters('valid');
        $params{merge} ? return $self->_run(-align_files =>\@ seq):
            return $self->_run(-seq_files =>\@ seq);
        return $self->_run(-seq_files =>\@ seq);
    }
}
cmemitdescriptionprevnextTop
sub cmemit {
    my ($self) = shift;
    $self->program('cmemit');
    return $self->_run(@_);
}
cmbuilddescriptionprevnextTop
sub cmbuild {
    my ($self,@seq) = @_;
    $self->program('cmbuild');
    if  (ref $seq[0] && $seq[0]->isa("Bio::Align::AlignI") ){# it is an object
        my $infile1 = $self->_writeAlignFile(@seq);
        return  $self->_run(-align_files => [$infile1]);
    } else {
        return  $self->_run(-align_files =>\@ seq);
    }
}
cmscoredescriptionprevnextTop
sub cmscore {
    my ($self,@seq) = @_;
    $self->program('cmscore');
    return  $self->_run();
}
cmcalibratedescriptionprevnextTop
sub cmcalibrate {
    my ($self,@seq) = @_;
    $self->program('cmcalibrate');
    return  $self->_run();
}
cmstatdescriptionprevnextTop
sub cmstat {
    my ($self,@seq) = @_;
    $self->program('cmstat');
    return  $self->_run();
}
set_parametersdescriptionprevnextTop
sub set_parameters {
    my $self = shift;
    # circumvent any issues arising from passing in refs
    my %args = (ref($_[0]) eq 'HASH')  ? %{$_[0]} :
               (ref($_[0]) eq 'ARRAY') ? @{$_[0]} :
               @_;
    # set the parameters passed in, but only ones supported for the program
    my ($prog, $validate) = ($self->program, $self->validate_parameters);

    # parameter cleanup
    %args = map { my $a = $_;
              $a =~ s{^-}{};
              lc $a => $args{$_}
                 } sort keys %args;
    
    while (my ($key, $val) = each %args) {
        if (exists $INFERNAL_PARAMS{$key}) {
            my ($type, $prefix) = @{$INFERNAL_PARAMS{$key}}[0..1];
            @{$self->{parameters}->{$key}} = ($type, $prefix);
            unshift @{$self->{parameters}->{$key}}, 
                $type eq 'param'          ? $val :
                $type eq 'switch' && $val ? 1 : 0;
            if ($validate) {
                my %in_exe = map {$_ => 1} @{$INFERNAL_PARAMS{$key}}[2..$#{$INFERNAL_PARAMS{$key}}];
                $self->warn("Parameter $key not used for $prog") if !exists $in_exe{$key};
            }
        } else {
            $self->warn("Parameter $key does not exist") if ($validate);
        }
    }
}
reset_parametersdescriptionprevnextTop
sub reset_parameters {
    my $self = shift;
    delete $self->{parameters};
    if (@_) {
        $self->set_parameters(@_);
    }
}
validate_parametersdescriptionprevnextTop
sub validate_parameters {
    my ($self) = shift;
    if (@_) {
        $self->{validate_params} = defined $_[0] ? 1 : 0;
    }
    return $self->{validate_params};
}
parameters_changeddescriptionprevnextTop
sub parameters_changed {
 1
}
available_parametersdescriptionprevnextTop
sub available_parameters {
    my ($self, $exec) = @_;
    my @params;
    if ($exec) {
        $self->throw("$exec is not part of the Infernal package") if !exists($INFERNAL_PROGRAM{$exec});
        for my $p (sort keys %INFERNAL_PARAMS) {
            if (grep { $exec eq $_ }
                @{$INFERNAL_PARAMS{$p}}[2..$#{$INFERNAL_PARAMS{$p}}])
            {
                push @params, $p;
            }
        }
    } else {
        @params = (sort keys %INFERNAL_PARAMS, sort keys %LOCAL_PARAMS);
    }
    return @params;
}
get_parametersdescriptionprevnextTop
sub get_parameters {
    my ($self, $option) = @_;
    $option ||= ''; # no option
    my %params;
    if (exists $self->{parameters}) {
        %params = (ref $option eq 'ARRAY') ? (
                    map {$_ => $self->{parameters}{$_}[0]}
                    grep { exists $self->{parameters}{$_} } @$option) :
                (lc $option eq 'full')     ?
                    (%{$self->{parameters}}) :
                (lc $option eq 'valid')    ?
                    (map {$_ => $self->{parameters}{$_}}
                    grep { exists $self->{valid_params}->{$_} } keys %{$self->{parameters}}) :
                (map {$_ => $self->{parameters}{$_}[0]} keys %{$self->{parameters}});
    } else {
        %params = ();
    }
    return %params;
}
to_exe_stringdescriptionprevnextTop
sub to_exe_string {
    my ($self, @passed) = @_;
    my ($seqs, $aligns) = $self->_rearrange([qw(SEQ_FILES ALIGN_FILES)], @passed);
    if ($seqs || $aligns) {
        $self->throw("Seqs or alignments must be an array reference") unless
            ($seqs && ref($seqs) eq 'ARRAY') || ($aligns && ref($aligns) eq 'ARRAY' );
    }
    
    my %args = map {$_ => []} qw(switch param input redirect);
    my %params = $self->get_parameters('valid');
    
    my ($exe, $prog, $model, $outfile) = ($self->executable,
                                   $self->program_name,
                                   $self->model_file,
                                   $self->outfile_name);
    
    $self->throw("Executable not found") unless defined($exe);
    
    delete $params{o} if exists $params{o};

    if (!defined($model) && $prog ne 'cmbuild') {
        $self->throw("model_file() not defined")
    }
    
    $outfile ||= '';
    
    for my $p (sort keys %params) {
        if ($params{$p}[0]) {
            my $val = $params{$p}[1] eq 'param' ? ' '.$params{$p}[0] : '';
            push @{$args{$params{$p}[1]}}, $params{$p}[2].$p.$val;
        }
    }
    
    # TODO: not sure what happens when we pass in multiple seq or alignment
    # filenames, may need checking 
    if ($prog eq 'cmscore' || $prog eq 'cmstat' || $prog eq 'cmcalibrate') {
        push @{$args{'redirect'}}, "> $outfile" if $outfile;
        push @{$args{'input'}}, $model;
    } elsif ($prog eq 'cmsearch') {
        if (!defined $seqs) {
            $self->throw('cmsearch requires a sequence file name');
        }
        push @{$args{'param'}}, "-o $outfile" if $outfile;
        push @{$args{'input'}}, ($model, @$seqs);
    } elsif ($prog eq 'cmalign') {
        if ($params{'merge'}) {
            $self->throw('cmalign with --merge option requires two alignment files') if
                !defined($aligns) || @$aligns < 2;
            push @{$args{'input'}}, ($model, @$aligns);
        } else {
            $self->throw('cmalign requires a sequence file') if
                !defined $seqs;
            push @{$args{'input'}}, ($model, @$seqs);
        }
        push @{$args{'param'}}, "-o $outfile" if $outfile;
    } elsif ($prog eq 'cmbuild') {
        $self->throw('cmbuild requires one alignment file') if
            !defined($aligns);
        if ($model) {
            push @{$args{'input'}}, ($model, @$aligns);
            push @{$args{'redirect'}}, "> $outfile" if $outfile;
        } else {
            push @{$args{'input'}}, ($outfile, @$aligns);
        }
    } elsif ($prog eq 'cmemit') {
        if (!$outfile) {
            $self->throw('cmemit requires an outfile_name; tempfile support not implemented yet');
        } else {
            push @{$args{'input'}}, ($model, ,$outfile);
        }
    }
    
    # quiet!
    if ($self->quiet && $prog ne 'cmsearch') {
        if ($prog eq 'cmalign') {
            push @{$args{switch}}, '-q' if !exists $params{q};
        } else {
            push @{$args{redirect}}, '> /dev/null';
        }
    }
    
    my $string = "$exe ".join(' ',(@{$args{switch}},
                                   @{$args{param}},
                                   @{$args{input}},
                                   @{$args{redirect}}));

    $string;
}

############### PRIVATE ###############

#=head2 _run
#
# Title   :   _run
# Usage   :   $obj->_run()
# Function:   Internal(not to be used directly)
# Returns :   
# Args    :
#
#=cut

{
    my %ALLOWED = map {$_ => 1} qw(run cmsearch cmalign cmemit cmbuild
    cmcalibrate cmstat cmscore);
}
_rundescriptionprevnextTop
sub _run {
    my ($self)= shift;
    
    my ($prog, $model, $out, $version) = ($self->program,
                                          $self->model_file,
                                          $self->outfile_name,
                                          $self->version);
    
    if (my $caller = (caller(1))[3]) {
        $caller =~ s{.*::(\w+)$}{$1};
        $self->throw("Calling _run() from disallowed method") unless exists $ALLOWED{$caller};
    } else {
        $self->throw("Can't call _run directly");
    }
    
    # a model and a file must be defined for all but cmemit; cmemit must have a
    # file or model defined (using $file if both are defined)
    
    # relevant files are passed on to the string builder
    my $str = $self->to_exe_string(@_);
    $self->debug("Infernal command: $str\n");
    
    my %has = $self->get_parameters('valid');
    
    my $obj =
        ($prog eq 'cmsearch') ? Bio::SearchIO->new(-format => 'infernal',
                                                -version => $version,
                                                -model => $model) :
        ($prog eq 'cmalign' )                              ? Bio::AlignIO->new(-format => 'stockholm') :
        ($prog eq 'cmemit' && $has{a}) ? Bio::AlignIO->new(-format => 'stockholm') :
        ($prog eq 'cmemit') ? Bio::SeqIO->new(-format => 'fasta') :
              undef;
    my @args;
    # file output
    if ($out) {
        my $status = system($str);
        if($status || !-e $out || -z $out ) {
            my $error = ($!) ? "$! Status: $status" : "Status: $status";
            $self->throw( "Infernal call crashed: $error\n [command $str]\n");
            return undef;
        }
        if ($obj && ref($obj)) {
            $obj->file($out);
            @args = (-file => $out);
        }
    # fh-based (no outfile)
    } else {
        open(my $fh,"$str |") || $self->throw("Infernal call ($str) crashed: $?\n");
        if ($obj && ref($obj)) {
            $obj->fh($fh);
            @args = (-fh => $fh);
        } else {
            # dump to debugging
            my $io;
            while(<$fh>) {$io .= $_;}
            close($fh);
            $self->debug($io) if $io;
            return 1;
        }
    }
    $obj->_initialize_io(@args) if $obj && ref($obj);
    return $obj || 1;
}
}
_writeSeqFiledescriptionprevnextTop
sub _writeSeqFile {
    my ($self,@seq) = @_;
    my ($tfh,$inputfile) = $self->io->tempfile(-dir=>$self->tempdir);
    my $in  = Bio::SeqIO->new(-fh => $tfh , '-format' => 'Fasta');
    foreach my $s(@seq){
    $in->write_seq($s);
    }
    $in->close();
    $in = undef;
    close($tfh);
    undef $tfh;
    return $inputfile;
}
_writeAlignFiledescriptionprevnextTop
sub _writeAlignFile {
    my ($self,@align) = @_;
    my ($tfh,$inputfile) = $self->io->tempfile(-dir=>$self->tempdir);
    my $in  = Bio::AlignIO->new('-fh'     => $tfh , 
                '-format' => 'stockholm');
    foreach my $s(@align){
        $in->write_aln($s);
    }
    $in->close();
    $in = undef;
    close($tfh);
    undef $tfh;
    return $inputfile;
}

# this is a private sub used to regenerate the class data structures,
# dumped to STDOUT

# could probably add in a description field if needed...
}
_dump_paramsdescriptionprevnextTop
sub _dump_params {
    my %params;
    my %usage;
    for my $exec (qw(cmalign cmbuild cmcalibrate cmemit cmscore cmsearch cmstat)) {
        my $output = `$exec --devhelp`;
        if ($?) {
            $output = `$exec -h`;
        }
        my @lines = split("\n",$output);
        
        for my $line (@lines) {
            next if $line =~ /^#/;
            if ($line =~ /^\s*(-{1,2})(\S+)\s+(<\S+>)?/) {
                my %data;
                ($data{prefix}, my $p, $data{arg}) = ($1, $2, $3 ? 'param' : 'switch');
                if (exists $params{$p}) {
                    if ($data{prefix} ne $params{$p}{prefix}) {
                        warn("$data{prefix} for $p in $exec doesn't match prefix for same parameter in ".$params{$p}{exec}[-1].":".$params{$p}{prefix});
                    }
                    if ($data{arg} ne $params{$p}{arg}) {
                        warn("$data{arg} for $p in $exec doesn't match arg for same parameter in ".$params{$p}{exec}[-1].":".$params{$p}{arg});
                    }
                }
                
                while (my ($key, $val) = each %data) {
                    $params{$p}->{$key} = $val;
                }
                push @{$params{$p}->{exec}}, $exec;
            } elsif ($line =~ /Usage:\s*(.+)$/) {
                push @{$usage{$exec}}, $1;
            } else {
                #print "$line\n";
            }
        }
    }

    # generate  data structure
    print "our %INFERNAL_PARAMS = (\n";
    for my $k (sort keys %params) {
        printf("  %-17s => [","'$k'");
        for my $sub (qw(arg prefix exec)) {
            my $str = (ref($params{$k}{$sub}) eq 'ARRAY') ?
                  "qw(".join(' ', @{$params{$k}{$sub}}).")" :
                  "'".$params{$k}{$sub}."',";
            printf("%-10s", $str);
        }
        print "],\n";
    }
    print ");\n\n";
    
    # generate usage data structure
    print "our %INFERNAL_PROGRAM = (\n";
    for my $k (sort keys %usage) {
        printf("  %-17s => [\n","'$k'");
        print '   '.join(",\n   ", map {"'$_'"} @{$usage{$k}})."\n";
        print "  ],\n";
    }
    print ");\n";

}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris FieldsTop
 Email: cjfields-at-uiuc-dot-edu
CONTRIBUTORS Top
 cjfields-at-uiuc-dot-edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Specific program interface methodsTop
Bio::ParameterBaseI-specific methodsTop
These methods are part of the Bio::ParameterBaseI interface
to_* methodsTop
All to_* methods are implementation-specific