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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::Motif
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6
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7 =head1 DESCRIPTION
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8
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9 'Funcgen::Motif'
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10
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11 TODO: Try to collate that to Funcgen
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12
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13 =cut
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14
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15
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16 package Bio::EnsEMBL::Funcgen::RunnableDB::Motif;
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17
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18 use warnings;
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19 use strict;
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20
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21 use base ('Bio::EnsEMBL::Hive::Process');
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22
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23 use Bio::EnsEMBL::DBSQL::DBAdaptor;
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24 use Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor;
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25 use Bio::EnsEMBL::Utils::Exception qw(throw warning stack_trace_dump);
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26 use Data::Dumper;
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27
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28 sub fetch_input { # nothing to fetch... just the parameters...
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29 my $self = shift @_;
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30
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31 $self->SUPER::fetch_input();
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32
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33 if(!$self->param('bin_dir')){ throw "No binary folder given"; }
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34 $self->_bin_folder($self->param('bin_dir'));
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35
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36 if(!$self->param('species')){ throw "No species given"; }
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37 $self->_species($self->param('species'));
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38
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39 if(!$self->param('bin_size')){ throw "No bin size given"; }
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40 $self->_bin_size($self->param('bin_size'));
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41
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42 if(!$self->param('window_size')){ throw "No window size given"; }
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43 $self->_window_size($self->param('window_size'));
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44
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45 #Get the core db... possibly make these non-mandatory
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46 if(!$self->param('dnadb_host')){ throw "No core host given"; }
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47 if(!$self->param('dnadb_port')){ throw "No core port given"; }
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48 if(!$self->param('dnadb_user')){ throw "No core user given"; }
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49 #if(!$self->param('dnadb_name')){ throw "No core dbname given"; }
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50 my $dba;
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51 eval{
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52 $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
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53 -host => $self->param('dnadb_host'),
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54 -port => $self->param('dnadb_port'),
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55 -user => $self->param('dnadb_user'),
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56 -dbname => $self->param('dnadb_name'),
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57 -species => $self->_species,
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58 );
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59 };
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60 if($@) { throw "Error creating the Core DB Adaptor: $@"; }
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61 if(!$dba){ throw "Could not connect to Core DB"; }
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62
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63 #Get the efg db... always read only user
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64 if(!$self->param('dbhost')){ throw "No host given"; }
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65 if(!$self->param('dbport')){ throw "No port given"; }
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66 if(!$self->param('dbuser')){ throw "No user given"; }
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67 if(!$self->param('dbname')){ throw "No dbname given"; }
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68 eval{
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69 $self->_efgdba(Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(
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70 -host => $self->param('dbhost'),
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71 -port => $self->param('dbport'),
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72 -user => $self->param('dbuser'),
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73 -dbname => $self->param('dbname'),
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74 -species => $self->_species,
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75 -dnadb => $dba,
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76 ));
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77 };
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78 if($@) { throw "Error creating the EFG DB Adaptor: $@"; }
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79 if(!$self->_efgdba()){ throw "Could not connect to EFG DB"; }
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80
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81 my $dnadbc = $self->_efgdba()->dnadb->dbc;
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82 warn $dnadbc->host." ".$dnadbc->port." ".$dnadbc->username." ".$dnadbc->dbname;
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83
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84
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85 if(!$self->param('feature_set')){ throw "No feature set given"; }
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86 my $fseta = $self->_efgdba()->get_FeatureSetAdaptor();
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87 my $fset = $fseta->fetch_by_name($self->param('feature_set'));
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88 if(!$fset){
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89 throw $self->param('feature_set')." is not a valid Feature Set";
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90 }
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91 $self->_feature_set($fset);
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92
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93 if(!$self->param('output_dir')){ throw "No output dir given"; }
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94 $self->_output_dir($self->param('output_dir')."/".$self->_feature_set->name);
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95
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96 return 1;
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97 }
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98
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99 sub run {
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100 my $self = shift @_;
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101
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102 return 1;
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103 }
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104
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105
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106 sub write_output { # Nothing is written at this stage (for the moment)
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107
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108 my $self = shift @_;
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109
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110 return 1;
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111
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112 }
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113
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114 #Private Generic getter and setter
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115 sub _getter_setter {
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116 my ($self, $param_name, $param_value) = @_;
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117 if(!$param_name){ return undef; }
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118 if(!$param_value){
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119 $param_value = $self->param($param_name);
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120 } else {
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121 $self->param($param_name, $param_value);
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122 }
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123 return $param_value;
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124 }
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125
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126 # Private getter / setters : Maybe do some validation in some cases...
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127
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128 #Private getter / setter to the bin folder
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129 sub _bin_folder {
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130 return $_[0]->_getter_setter('bin_folder',$_[1]);
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131 }
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132
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133 #Private getter / setter to the EFG DB Adaptor
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134 sub _efgdba {
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135 return $_[0]->_getter_setter('efgdb',$_[1]);
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136 }
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137
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138 #Private getter / setter to the bin size
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139 sub _bin_size {
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140 return $_[0]->_getter_setter('bin_size',$_[1]);
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141 }
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142
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143 #Private getter / setter to the window size
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144 sub _window_size {
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145 return $_[0]->_getter_setter('window_size',$_[1]);
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146 }
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147
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148 #Private getter / setter to the output dir
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149 sub _output_dir {
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150 return $_[0]->_getter_setter('output_dir',$_[1]);
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151 }
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152
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153 #Private getter / setter to the feature set
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154 sub _feature_set {
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155 return $_[0]->_getter_setter('feature_set',$_[1]);
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156 }
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157
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158 #Private getter / setter to the species
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159 sub _species {
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160 return $_[0]->_getter_setter('species',$_[1]);
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161 }
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162
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163 1;
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