Raw content of Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DumpDnaCollection
<![CDATA[#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DumpDnaCollection
=cut
=head1 SYNOPSIS
=cut
=head1 DESCRIPTION
=cut
=head1 CONTACT
Abel Ureta-Vidal <abel@ebi.ac.uk>
=cut
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::DumpDnaCollection;
use strict;
use Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor;;
use Bio::EnsEMBL::Utils::Exception;
use Time::HiRes qw(time gettimeofday tv_interval);
use Bio::EnsEMBL::Analysis::Runnable::Blat;
#use Bio::EnsEMBL::Pipeline::Runnable::Blat;
#our @ISA = qw(Bio::EnsEMBL::Pipeline::RunnableDB);
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Hive::Process;
our @ISA = qw(Bio::EnsEMBL::Hive::Process);
my $DEFAULT_DUMP_MIN_SIZE = 11500000;
=head2 fetch_input
Title : fetch_input
Usage : $self->fetch_input
Function: Fetches input data for repeatmasker from the database
Returns : none
Args : none
=cut
sub fetch_input {
my( $self) = @_;
#create a Compara::DBAdaptor which shares the same DBI handle
#with $self->db (Hive DBAdaptor)
$self->{'comparaDBA'} = Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor->new(-DBCONN=>$self->db->dbc);
$self->get_params($self->parameters);
$self->get_params($self->input_id);
throw("Missing dna_collection_name") unless($self->dna_collection_name);
unless ($self->dump_min_size) {
$self->dump_min_size($DEFAULT_DUMP_MIN_SIZE);
}
#must have dump_nib or dump_ooc defined
throw("Missing dump_nib or dump_ooc method or dump_dna") unless ($self->dump_nib || $self->dump_dna);
return 1;
}
sub run
{
my $self = shift;
if ($self->dump_nib) {
$self->dumpNibFiles;
}
if ($self->dump_dna) {
$self->dumpDnaFiles;
}
return 1;
}
sub write_output {
my( $self) = @_;
return 1;
}
##########################################
#
# getter/setter methods
#
##########################################
sub dna_collection_name {
my $self = shift;
$self->{'_dna_collection_name'} = shift if(@_);
return $self->{'_dna_collection_name'};
}
sub dump_dna {
my $self = shift;
$self->{'_dump_dna'} = shift if(@_);
return $self->{'_dump_dna'};
}
sub dump_nib {
my $self = shift;
$self->{'_dump_nib'} = shift if(@_);
return $self->{'_dump_nib'};
}
sub dump_min_size {
my $self = shift;
$self->{'_dump_min_size'} = shift if(@_);
return $self->{'_dump_min_size'};
}
##########################################
#
# internal methods
#
##########################################
sub get_params {
my $self = shift;
my $param_string = shift;
return unless($param_string);
#print("parsing parameter string : ",$param_string,"\n");
my $params = eval($param_string);
return unless($params);
if(defined($params->{'dna_collection_name'})) {
$self->dna_collection_name($params->{'dna_collection_name'});
}
if(defined($params->{'dump_min_size'})) {
$self->dump_min_size($params->{'dump_min_size'});
}
if(defined($params->{'dump_dna'})) {
$self->dump_dna($params->{'dump_dna'});
}
if(defined($params->{'dump_nib'})) {
$self->dump_nib($params->{'dump_nib'});
}
return 1;
}
sub dumpNibFiles {
my $self = shift;
$self->{'comparaDBA'}->dbc->disconnect_when_inactive(1);
my $starttime = time();
my $dna_collection = $self->{'comparaDBA'}->get_DnaCollectionAdaptor->fetch_by_set_description($self->dna_collection_name);
my $dump_loc = $dna_collection->dump_loc;
unless (defined $dump_loc) {
throw("dump_loc directory is not defined, can not dump nib files\n");
}
foreach my $dna_object (@{$dna_collection->get_all_dna_objects}) {
if($dna_object->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunkSet')) {
warn "At this point you should get DnaFragChunk objects not DnaFragChunkSet objects!\n";
next;
}
if($dna_object->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunk')) {
next if ($dna_object->length <= $self->dump_min_size);
my $nibfile = "$dump_loc/". $dna_object->dnafrag->name . ".nib";
#don't dump nibfile if it already exists
next if (-e $nibfile);
my $fastafile = "$dump_loc/". $dna_object->dnafrag->name . ".fa";
#$dna_object->dump_to_fasta_file($fastafile);
#use this version to solve problem of very large chromosomes eg opossum
$dna_object->dump_chunks_to_fasta_file($fastafile);
system("faToNib", "$fastafile", "$nibfile") and throw("Could not convert fasta file $fastafile to nib: $!\n");
#hack to use newer version of faToNib to dump larger fa files eg cow Un.fa
#system("/nfs/team71/phd/klh/progs/kent/bin/i386_64/faToNib", "$fastafile", "$nibfile") and throw("Could not convert fasta file $fastafile to nib: $!\n");
unlink $fastafile;
$dna_object = undef;
}
}
if($self->debug){printf("%1.3f secs to dump nib for \"%s\" collection\n", (time()-$starttime), $self->collection_name);}
$self->{'comparaDBA'}->dbc->disconnect_when_inactive(0);
return 1;
}
sub dumpDnaFiles {
my $self = shift;
$self->{'comparaDBA'}->dbc->disconnect_when_inactive(1);
my $starttime = time();
my $dna_collection = $self->{'comparaDBA'}->get_DnaCollectionAdaptor->fetch_by_set_description($self->dna_collection_name);
my $dump_loc = $dna_collection->dump_loc;
unless (defined $dump_loc) {
throw("dump_loc directory is not defined, can not dump nib files\n");
}
foreach my $dna_object (@{$dna_collection->get_all_dna_objects}) {
if($dna_object->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunkSet')) {
my $first_dna_object = $dna_object->get_all_DnaFragChunks->[0];
my $chunk_array = $dna_object->get_all_DnaFragChunks;
my $name = $first_dna_object->dnafrag->name . "_" . $first_dna_object->seq_start . "_" . $first_dna_object->seq_end;
my $fastafile = "$dump_loc/". $name . ".fa";
#Must always dump new fasta files because different runs call the chunks
#different names and the chunk name is what is stored in the fasta file.
if (-e $fastafile) {
unlink $fastafile
}
foreach my $chunk (@$chunk_array) {
#A chunk_set will contain several seq_regions which will be appended
#to a single fastafile. This means I can't use
#dump_chunks_to_fasta_file because this deletes the fastafile each
#time!
$chunk->dump_to_fasta_file(">".$fastafile);
}
}
if($dna_object->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunk')) {
next if ($dna_object->length <= $self->dump_min_size);
my $name = $dna_object->dnafrag->name . "_" . $dna_object->seq_start . "_" . $dna_object->seq_end;
my $fastafile = "$dump_loc/". $name . ".fa";
if (-e $fastafile) {
unlink $fastafile
}
$dna_object->dump_to_fasta_file(">".$fastafile);
}
$dna_object = undef;
}
if($self->debug){printf("%1.3f secs to dump nib for \"%s\" collection\n", (time()-$starttime), $self->collection_name);}
$self->{'comparaDBA'}->dbc->disconnect_when_inactive(0);
return 1;
}
#Xreate a ooc file used in blat analysis. Not used for translated blat.
sub create_ooc_file {
my ($dir, $seq_region) = @_;
my $ooc_file = "$dir/$seq_region/5ooc";
#make new directory to store 5ooc file for each seq_region
if (!-e "$dir/$seq_region") {
mkdir("$dir/$seq_region")
or throw("Directory $dir/$seq_region cannot be created");
}
my $runnable = new Bio::EnsEMBL::Analysis::Runnable::Blat (
-database => "$dir/$seq_region.fa",
-query_type => "dnax",
-target_type => "dnax",
-options => "-ooc=$ooc_file -tileSize=5 -makeOoc=$ooc_file -mask=lower -qMask=lower");
$runnable->run;
return $ooc_file;
}
1;
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