#
# BioPerl module for Bio::Tools::Run::ERPIN
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::ERPIN - Wrapper for local execution of the ERPIN suite of
programs.
=head1 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 => 'Ðumask 4 Ðadd 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,
$hsp->score,
)), "\n";
}
}
}
=head1 DESCRIPTION
=cut
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Chris Fields
Email: cjfields-at-uiuc-dot-edu
=head1 CONTRIBUTORS
cjfields-at-uiuc-dot-edu
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Tools::Run::ERPIN;
use strict;
use Bio::SeqIO;
use Bio::Root::Root;
use Bio::SearchIO;
use Bio::AlignIO;
use Bio::Tools::Run::WrapperBase;
use base qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
# will move parameters to each program, use this for _set_params
my %ERPIN_PROGS = (
cfgs => 1,
erpin => 1,
frandseq => 1,
mstat => 1,
sview => 1,
tstrip => 1,
epnstat => 1,
ev => 1,
mhistview => 1,
pview => 1,
tstat => 1,
tview => 1,
);
my %ERPIN_SWITCHES = map {$_ => 1} qw(dmp smp fwd rev fwd+rev long short mute
warnings globstat locstat unifstat Eon Eoff hist chrono);
# order is important here
my @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);
=head2 new
Title : new
Usage : my $wrapper = Bio::Tools::Run::RNAMotif->new(@params)
Function: creates a new RNAMotif factory
Returns: Bio::Tools::Run::RNAMotif
Args : list of parameters
-tempfile => set tempfile flag (default 0)
-outfile_name => set file to send output to (default none)
=cut
sub new {
my ($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;
}
=head2 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
my ($self) = shift;
return $self->program(@_);
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{ERPINDIR}) if $ENV{ERPINDIR};
}
=head2 version
Title : version
Usage : $v = $prog->version();
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
=cut
sub version {
my ($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;
}
=head2 run
Title : run
Usage : $obj->run($seqFile)
Function: Runs ERPIN programs and returns Bio::SearchIO
Returns :
Args : Must pass Bio::PrimarySeqI's or file names
=cut
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") ){# it is an object
my $infile1 = $self->_writeSeqFile(@seq);
return $self->_run($infile1);
} else {
return $self->_run(@seq);
}
}
=head2 tempfile
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
=cut
sub tempfile {
my $self = shift;
return $self->{'_tempfile'} = shift if @_;
return $self->{'_tempfile'};
}
=head2 _run
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns :
Args :
=cut
sub _run {
my ($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");
# rnamotif => SearchIO object
# rmfmt -a => AlignIO object
# all others sent to outfile, tempfile, or STDERR (upon verbose = 1)
my $obj = ($progname eq 'erpin') ?
Bio::SearchIO->new(-verbose => $self->verbose,
-format => "erpin",
-version => $self->version,
-database => $file
) :
undef;
my @args;
# file-based
if ($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);
}
# fh-based
} else {
open(my $fh,"$str |") || $self->throw("ERPIN call ($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;
}
}
# initialize SearchIO/AlignIO...um...IO
# (since file/fh set post obj construction)
$obj->_initialize_io(@args) if $obj && ref($obj);
return $obj || 1;
}
=head2 _setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: creates a string of params to be used in the command string
Example :
Returns : string of params
Args :
=cut
sub _setparams {
my ($self, $file) = @_;
my $progname = $self->program_name;
# small sanity check
$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 $param_string;
}
=head2 _writeSeqFile
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns : writes passed Seq objects to tempfile, to be used as input
for program
Args :
=cut
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;