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1 =pod
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2
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3 =head1 NAME
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4
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5 Bio::EnsEMBL::Funcgen::RunnableDB::Alignment;
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6
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7 =head1 DESCRIPTION
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8
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9 'Alignment' Is a base class for other classes dealing with Alignment
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10 It contains virtually nothing so it may disappear and just pass to Funcgen
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11
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12 =cut
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13
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14 package Bio::EnsEMBL::Funcgen::RunnableDB::Alignment;
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15
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16 use warnings;
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17 use strict;
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18 use Bio::EnsEMBL::Funcgen::Utils::Helper;
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19 use Bio::EnsEMBL::DBSQL::DBAdaptor;
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20 use Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor;
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21 use Bio::EnsEMBL::Funcgen::InputSet;
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22 use Bio::EnsEMBL::Funcgen::DataSet;
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23 use Bio::EnsEMBL::Funcgen::FeatureSet;
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24 use Bio::EnsEMBL::Funcgen::AnnotatedFeature;
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25
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26 use base ('Bio::EnsEMBL::Funcgen::RunnableDB::Funcgen');
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27
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28 use Bio::EnsEMBL::Utils::Exception qw(throw warning stack_trace_dump);
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29 use Data::Dumper;
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30
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31 sub fetch_input {
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32 my $self = shift @_;
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33
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34 $self->param("file_type","sam");
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35
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36 $self->SUPER::fetch_input();
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37
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38 #Just override input folders... maybe consider overriding output folders too?
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39 my $input_dir = $self->_work_dir()."/fastq/".$self->_species()."/".$self->_experiment_name()."/".
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40 $self->_cell_type()->name."_".$self->_feature_type()->name;
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41 $self->_input_dir($input_dir);
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42
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43 #Folder where to send the final results...
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44 my $repository = $self->_work_dir()."/alignments/".$self->_species."/".$self->_assembly()."/".$self->_experiment_name();
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45 $self->_repository($repository);
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46
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47 return 1;
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48 }
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49
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50 #Private getter / setter to the input folder
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51 sub _input_dir {
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52 return $_[0]->_getter_setter('input_dir',$_[1]);
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53 }
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54
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55 #Private getter / setter to the repository folder
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56 sub _repository {
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57 return $_[0]->_getter_setter('repository',$_[1]);
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58 }
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59
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60 #Private getter / setter to an input file
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61 sub _input_file {
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62 return $_[0]->_getter_setter('input_file',$_[1]);
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63 }
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64
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65
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66 1;
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67
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