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 $self->{'_model_file'};
}
program_dirdescriptionprevnextTop
sub program_dir {
    return Bio::Root::IO->catfile($ENV{INFERNALDIR}) if $ENV{INFERNALDIR};
}
versiondescriptionprevnextTop
sub version {
    my ($self) = @_;
    return unless $self->executable;
    my $string = `cmsearch -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);
    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); 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
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  bioperl-l@bioperl.org                  - General discussion
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Support Top
 
Please direct usage questions or support issues to the mailing list:

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rather than to the module maintainer directly. Many experienced and
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Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
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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