# BioPerl module for Bio::Tools::Run::Alignment::Sim4
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Alignment::Sim4 - Wrapper for Sim4 program that allows
for alignment of cdna to genomic sequences
=head1 SYNOPSIS
use Bio::Tools::Run::Alignment::Sim4;
my @params = (W=>15,K=>17,D=>10,N=>10,cdna_seq=>"mouse_cdna.fa",genomic_seq=>"mouse_genomic.fa");
my $sim4 = Bio::Tools::Run::Alignment::Sim4->new(@params);
my @exon_sets = $sim4->align;
foreach my $set(@exon_sets){
foreach my $exon($set->sub_SeqFeature){
print $exon->start."\t".$exon->end."\t".$exon->strand."\n";
print "\tMatched ".$exon->est_hit->seq_id."\t".$exon->est_hit->start."\t".$exon->est_hit->end."\n";
}
}
One can also provide a est database
$sio = Bio::SeqIO->new(-file=>"est.fa",-format=>"fasta");
@est_seq=();
while(my $seq = $sio->next_seq){
push @est_seq,$seq;
}
my @exon_sets = $factory->align(\@est_seq,$genomic);
=head1 DESCRIPTION
Sim4 program is developed by Florea et al. for aligning cdna/est
sequence to genomic sequences
Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W.
A computer program for aligning a cDNA sequence with a genomic DNA sequence.
Genome Res 1998 Sep;8(9):967-74
The program is available for download here:
http://globin.cse.psu.edu/
=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 - Shawn Hoon
Email shawnh@fugu-sg.org
=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::Alignment::Sim4;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
@SIM4_PARAMS @OTHER_PARAMS @OTHER_SWITCHES %OK_FIELD);
use strict;
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Tools::Run::WrapperBase;
use Bio::Tools::Sim4::Results;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
# You will need to enable Sim4 to find the Sim4 program. This
# can be done in (at least) two ways:
#
# 1. define an environmental variable SIM4DIR
# export SIM4DIR =/usr/local/share/sim4
# where the sim4 package is installed
#
# 2. include a definition of an environmental variable SIM4 in
# every script that will use Sim4.pm
# $ENV{SIMR4DIR} = '/usr/local/share/sim4';
BEGIN {
@SIM4_PARAMS= qw(A W X K C R D H P N B);
@OTHER_PARAMS= qw(CDNA_SEQ GENOMIC_SEQ OUTFILE);
@OTHER_SWITCHES = qw(SILENT QUIET VERBOSE);
# Authorize attribute fields
foreach my $attr ( @SIM4_PARAMS, @OTHER_PARAMS,
@OTHER_SWITCHES) { $OK_FIELD{$attr}++; }
}
=head2 program_name
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'sim4';
}
=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{SIM4DIR}) if $ENV{SIM4DIR};
}
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
# to facilitiate tempfile cleanup
$self->io->_initialize_io();
$self->A(0); # default
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
if ($attr =~/est_first/i ) { #NEW
$self->{est_first} = $value; #NEW
next; #NEW
} #NEW
next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~/'PROGRAM'/i ) {
$self->executable($value);
next;
}
$self->$attr($value);
}
return $self;
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$attr = uc $attr;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 version
Title : version
Usage : not supported
Function: Cannot determine from program
Example :
Returns : float or undef
Args : none
=cut
sub version {
my ($self) = @_;
return undef;
}
=head2 align
Title : align
Usage :
$cdna = 't/data/cdna.fa';
$genomic = 't/data/cdna.fa';
@exon_set = $factory->align($cdna,$genomic);
or
#@seq_array is array of Seq objs
$cdna = \@seq_array;
@exon_set = $factory->align($cdna,$genomic);
of
@exon_set = $factory->align($cdna->[0],$genomic)
Function: Perform a Sim4 alignment
Returns : An array of Bio::SeqFeature::Generic objects which has
exons as sub seqfeatures.
Args : Name of two files containing fasta sequences,
or 2 Bio::SeqI objects
or a combination of both
first is assumed to be cdna
second is assumed to be genomic
More than one cdna may be provided. If an object,
assume that its an array ref.
=cut
sub align {
my ($self,$cdna,$genomic) = @_;
$self->cdna_seq($cdna) if $cdna;
$self->throw("Need to provide a cdna sequence") unless $self->cdna_seq;
$self->genomic_seq($genomic) if $genomic;
$self->throw("Need to provide a genomic sequence") unless $self->genomic_seq;
my ($temp,$infile1, $infile2, $est_first,$seq);
my ($attr, $value, $switch);
# Create input file pointer
($est_first,$infile1,$infile2)= $self->_setinput($self->cdna_seq,$self->genomic_seq);
if (!($infile1 && $infile2)) {$self->throw("Bad input data (sequences need an id ) or less than 2 sequences in align!");}
# Create parameter string to pass to Sim4 program
my $param_string = $self->_setparams();
# run Sim4
my @exon_sets = $self->_run($est_first,$infile1,$infile2,$param_string);
return @exon_sets;
}
#################################################
#internal methods
=head2 _run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to Sim4 program
Example :
Returns : nothing; Sim4 output is written to a temp file
Args : Name of a file containing a set of unaligned fasta sequences
and hash of parameters to be passed to Sim4
=cut
sub _run {
my ($self,$estfirst,$infile1,$infile2,$param_string) = @_;
my $instring;
$self->debug( "Program ".$self->executable."\n");
if(! $self->outfile){
my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir);
close($tfh);
undef $tfh;
$self->outfile($outfile);
}
my $outfile = $self->outfile();
my $commandstring = $self->executable." $infile1 $infile2 $param_string > $outfile";
if($self->quiet || $self->silent || ($self->verbose < 0)){
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
$commandstring .= " 2>$null";
}
$self->debug( "Sim4 command = $commandstring");
my $status = system($commandstring);
$self->throw( "Sim4 call ($commandstring) crashed: $? \n") unless $status==0;
#use Sim4 parser
my $sim4_parser = Bio::Tools::Sim4::Results->new(-file=>$outfile,-estfirst=>$estfirst);
my @out;
while(my $exonset = $sim4_parser->next_exonset){
push @out, $exonset;
}
return @out;
}
=head2 _setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for Sim4 program
Example :
Returns : name of file containing Sim4 data input
Args : Seq or Align object reference or input file name
=cut
sub _setinput {
my ($self, $cdna,$genomic) = @_;
my ($infilename, $seq, $temp, $tfh1,$tfh2,$outfile1,$outfile2);
#my $estfirst=1;
my $estfirst= defined($self->{est_first}) ? $self->{_est_first} : 1;
my ($cdna_file,$genomic_file);
#a sequence obj
if(ref($cdna)) {
my @cdna = ref $cdna eq "ARRAY" ? @{$cdna} : ($cdna);
($tfh1,$cdna_file) = $self->io->tempfile(-dir=>$self->tempdir);
my $seqio = Bio::SeqIO->new(-fh=>$tfh1,-format=>'fasta');
foreach my $c (@cdna){
$seqio->write_seq($c);
}
close $tfh1;
undef $tfh1;
#if we have a est database, then input will go second
if($#cdna > 0){
$estfirst=0;
}
}
else {
my $sio = Bio::SeqIO->new(-file=>$cdna,-format=>"fasta");
my $count = 0;
while(my $seq = $sio->next_seq){
$count++;
}
$estfirst = $count > 1 ? 0:1;
$cdna_file = $cdna;
}
if( ref($genomic) ) {
($tfh1,$genomic_file) = $self->io->tempfile(-dir=>$self->tempdir);
my $seqio = Bio::SeqIO->new(-fh=>$tfh1,-format=>'fasta');
$seqio->write_seq($genomic);
close $tfh1;
undef $tfh1;
}
else {
$genomic_file = $genomic;
}
return ($estfirst,$cdna_file,$genomic_file) if $estfirst;
return ($estfirst,$genomic_file,$cdna_file);
}
=head2 _setparams()
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for Sim4 program
Example :
Returns : parameter string to be passed to Sim4
during align or profile_align
Args : name of calling object
=cut
sub _setparams {
my ($attr, $value, $self);
$self = shift;
my $param_string = "";
for $attr ( @SIM4_PARAMS ) {
$value = $self->$attr();
next unless (defined $value);
my $attr_key = uc $attr; #put params in format expected by Sim4
$attr_key = ' '.$attr_key;
$param_string .= $attr_key.'='.$value;
}
return $param_string;
}
1; # Needed to keep compiler happy