Bio::Tools::Run
ERPIN
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Summary
Bio::Tools::Run::ERPIN - Wrapper for local execution of the ERPIN suite of
programs.
Package variables
Privates (from "my" definitions)
%ERPIN_PROGS = ( cfgs => 1, erpin => 1, frandseq => 1, mstat => 1, sview => 1, tstrip => 1, epnstat => 1, ev => 1, mhistview => 1, pview => 1, tstat => 1, tview => 1, )
%ERPIN_SWITCHES = map {$_ => 1} qw(dmp smp fwd rev fwd+rev long short mute warnings globstat locstat unifstat Eon Eoff hist chrono)
@ERPIN_PARAMS = qw(program model file strategy dmp smp fwd rev fwd+rev long short mute warnings globstat locstat unifstat Eon Eoff hist seq1 nseq bgn len logzero tablen chrono pcw hpcw spcw sumf tset)
Included modules
Bio::AlignIO
Bio::Root::Root
Bio::SearchIO
Bio::SeqIO
Bio::Tools::Run::WrapperBase
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
Synopsis
#run
my @params = (
trset => 'BL.erpin',
region => [1, 10],
# Set up search strategy this way...
strategy => [ 'umask' => [1, 2],
'umask' => [1, 2, 3, 4],
'umask' => [1, 2, 3, 4, 5, 6],
'nomask',
'cutoff' => [0, 10, 15, 20]
]
# or use a simple string...
#strategy => 'Ğumask 4 Ğadd 5 -nomask -cutoff 0 10 15',
pcw => 100
);
my $factory = Bio::Tools::Run::ERPIN->new(-program =>'erpin',
@params);
# Pass the factory a Bio::Seq object or a file name
# Returns a Bio::SearchIO object
#my $search = $factory->run("B_sub.fas");
my $search = $factory->run($seq);
my @feat;
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
Methods
Methods description
Title : new
Usage : my $wrapper = Bio::Tools::Run::RNAMotif->new(@params)
Function: creates a new RNAMotif factory
Returns: Bio::Tools::Run::RNAMotif
Args : list of parameters
-tempfile => set tempfile flag (default 0)
-outfile_name => set file to send output to (default none) |
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None |
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args : |
Title : version
Usage : $v = $prog->version();
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none |
Title : run
Usage : $obj->run($seqFile)
Function: Runs ERPIN programs and returns Bio::SearchIO
Returns :
Args : Must pass Bio::PrimarySeqI's or file names |
Title : tempfile
Usage : $obj->tempfile(1)
Function: Set tempfile flag. When set, writes output to a tempfile; this
is overridden by outfile_name() if set
Returns : Boolean setting (or undef if not set)
Args : [OPTIONAL] Boolean |
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns :
Args : |
Title : _setparams
Usage : Internal function, not to be called directly
Function: creates a string of params to be used in the command string
Example :
Returns : string of params
Args : |
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns : writes passed Seq objects to tempfile, to be used as input
for program
Args : |
Methods code
sub new
{ my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($out, $tf) = $self->_rearrange([qw(OUTFILE_NAME TEMPFILE)], @args);
$self->io->_initialize_io();
if ($tf && !$out) {
my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir());
close($tfh);
undef $tfh;
$self->outfile_name($outfile);
} else {
$out ||= '';
$self->outfile_name($out);
}
$tf && $self->tempfile($tf);
$self->_set_from_args(\@args,
-methods => [@ERPIN_PARAMS],
-create => 1
);
return $self;} | sub program_name
{ my ($self) = shift;
return $self->program(@_); } | sub program_dir
{ return Bio::Root::IO->catfile($ENV{ERPINDIR}) if $ENV{ERPINDIR};} | sub version
{ my ($self) = @_;
return undef unless $self->executable;
my $string = `erpin -h 2>&1`;
my $v;
if ($string =~ m{Version\s([\d.]+)}) {
$v = $1;
}
return $self->{'_progversion'} = $v || $string;} | sub run
{ my ($self,@seq) = @_;
$self->throw ("Must define 'db', pass a file name, or a list of Bio::PrimarySeqI objects")
if (!@seq);
if (ref $seq[0] && $seq[0]->isa("Bio::PrimarySeqI") ){
my $infile1 = $self->_writeSeqFile(@seq);
return $self->_run($infile1);
} else {
return $self->_run(@seq);
}} | sub tempfile
{ my $self = shift;
return $self->{'_tempfile'} = shift if @_;
return $self->{'_tempfile'};} | sub _run
{ my ($self,$file,$prog) = @_;
return unless $self->executable;
$self->io->_io_cleanup();
my ($str, $progname, $outfile) =
($prog || $self->executable, $self->program_name, $self->outfile_name);
my $param_str = $self->_setparams($file);
$str .= " $param_str";
$self->debug("ERPIN command: $str\n");
my $obj = ($progname eq 'erpin') ?
Bio::SearchIO->new(-verbose => $self->verbose,
-format => "erpin",
-version => $self->version,
-database => $file
) :
undef;
my @args;
if ($outfile) {
local $SIG{CHLD} = 'DEFAULT';
my $status = system($str);
if($status || !-e $outfile || -z $outfile ) {
my $error = ($!) ? "$! Status: $status" : "Status: $status";
$self->throw( "ERPIN call crashed: $error\n [command $str]\n");
return undef;
}
if ($obj && ref($obj)) {
$obj->file($outfile);
@args = (-file => $outfile);
}
} else {
open(my $fh,"$str |") || $self->throw("ERPIN call ($str) crashed: $?\n");
if ($obj && ref($obj)) {
$obj->fh($fh);
@args = (-fh => $fh);
} else {
my $io;
while(<$fh>) {$io .= $_;}
close($fh);
$self->debug($io);
return 1;
}
}
$obj->_initialize_io(@args) if $obj && ref($obj);
return $obj || 1;} | sub _setparams
{ my ($self, $file) = @_;
my $progname = $self->program_name;
$self->throw("Unknown program: $progname") if
(!exists $ERPIN_PROGS{$progname} );
my $param_string;
my $outfile = ($self->outfile_name) ? ' > '.$self->outfile_name : '';
my ($tset, $st) = ($self->tset, $self->strategy);
$param_string = join " ", ($tset, $file, $st);
$self->debug("String : $param_string\n");
$self->throw("Must have both a training set and search strategy defined!")
if (!defined($tset) || !defined ($st));
my @params;
foreach my $attr (@ERPIN_PARAMS) {
next if $attr eq 'program' || $attr eq 'tset' || $attr eq 'strategy';
my $value = $self->$attr();
next unless ($attr eq 'file' || defined $value);
my $attr_key = '-'.$attr;
if (exists $ERPIN_SWITCHES{$attr}) {
push @params, $attr_key;
} else {
if ($attr eq 'file') {
push @params, $file;
} else {
push @params, $attr_key.' '.$value;
}
}
}
$param_string .= ' '.join ' ', @params;
$param_string .= $outfile if $outfile;
return $param_string;} | sub _writeSeqFile
{ my ($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;
}
1;} | General documentation
User feedback is an integral part of the evolution of this and other
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bioperl-l@bioperl.org - General discussion
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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
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address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Email: cjfields-at-uiuc-dot-edu
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _