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# Bio/RNA/Treekin/PopulationDataRecord.pm |
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package Bio::RNA::Treekin::PopulationDataRecord; |
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our $VERSION = '0.04'; |
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use 5.006; |
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use strict; |
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use warnings; |
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use Moose; |
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30731
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use MooseX::StrictConstructor; |
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13410
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use namespace::autoclean; |
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use autodie qw(:all); |
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use Scalar::Util qw(reftype looks_like_number); |
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use List::Util qw(max all); |
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use overload '""' => \&stringify; |
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has 'time' => (is => 'ro', required => 1); |
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has '_populations' => ( |
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is => 'ro', |
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required => 1, |
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init_arg => 'populations', |
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); |
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# Return a deep copy of this object. |
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sub clone { |
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my $self = shift; |
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my $clone = __PACKAGE__->new( |
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time => $self->time, |
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populations => [ $self->populations ], |
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); |
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return $clone; |
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} |
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# Return number of minima for which there is population data. |
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sub min_count { |
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321
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321
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573
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my $self = shift; |
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321
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506
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my $min_count = @{ $self->_populations }; # number of data points |
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13227
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1367
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return $min_count; |
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} |
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# Use to adjust the min count, e.g. when the passed data array was |
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# constructed before the number of minima was known. It may not be |
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# shrinked as data might be lost. |
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sub set_min_count { |
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1
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my ($self, $new_min_count) = @_; |
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51
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my $current_min_count = @{ $self->_populations }; |
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129
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confess 'Can only increase min_count' |
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if $current_min_count > $new_min_count; |
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55
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# Set additional states to population of 0. |
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for my $i ( $current_min_count..($new_min_count-1) ) { |
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483
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$self->_populations->[$i] = 0.; |
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} |
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60
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4
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116
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return; |
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} |
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63
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# Return populations of all mins. Use of_min() instead to get the |
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# population of a specific min. |
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# Returns a list of all minima's populations. |
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sub populations { |
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0
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1
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my $self = shift; |
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0
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0
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return @{ $self->_populations }; |
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69
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} |
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71
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# Get population for the given minimum. |
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sub of_min { |
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306
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306
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1
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168294
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my ($self, $min) = @_; |
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75
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306
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1144
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confess "Minimum $min is out of bounds" |
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if $min < 1 or $min > $self->min_count; |
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78
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# Minimum 1 is the first one (index 0) |
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306
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10015
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my $population = $self->_populations->[$min-1]; |
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306
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1675
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return $population; |
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} |
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83
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# Transform (reorder and resize) the population data according to a given |
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# mapping and resize to a given minimum count. All minima that are not |
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# mapped to a new position are discarded (replaced by zero). |
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# NOTE: Ensure that no two minima are mapped to the same position or crap |
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# will happen. |
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# Arguments: |
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# maps_to_min_ref: Hash ref that specifies for each kept minimum (key) to |
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# which new minimum (value) it is supposed to be mapped. |
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# new_min_count: New size (number of mins) of the record after the |
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# transformation. Defaults to the maximum value of maps_to_min_ref. |
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# Void. |
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sub transform { |
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1
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my ($self, $maps_to_min_ref, $new_min_count) = @_; |
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97
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# If not explicitely given, use max value a min was mapped to as min count. |
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0
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$new_min_count //= max values %$maps_to_min_ref; |
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100
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0
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0
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my @new_pops = (0) x $new_min_count; # new array with right size |
101
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0
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0
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my @source_mins = grep { defined $maps_to_min_ref->{$_} } |
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102
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1..$self->min_count; # filter unmapped |
103
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my @source_indices = map { $_ - 1 } @source_mins; |
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104
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my @target_indices = map { $maps_to_min_ref->{$_} - 1 } @source_mins; |
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105
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106
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# Sanity check. |
107
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confess "Cannot reorder as some minima are not mapped correctly" |
108
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0
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0
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unless all {$_ >= 0 and $_ < $new_min_count} @target_indices; |
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109
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110
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# Copy population data to the correct positions and overwrite original. |
111
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0
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0
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@new_pops[@target_indices] = @{$self->_populations}[@source_indices]; |
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0
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0
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112
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0
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@{ $self->_populations } = @new_pops; |
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0
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0
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113
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114
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0
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0
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return; |
115
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} |
116
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117
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sub _parse_population_data_line { |
118
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161
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161
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423
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my ($self, $population_data_line) = @_; |
119
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120
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161
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2409
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my ($time, @populations) = split /\s+/, $population_data_line; |
121
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122
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# Sanity checks. |
123
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161
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100
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727
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confess "No population data found in line:\n$population_data_line\n" |
124
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unless @populations; |
125
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160
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50
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572
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confess "Time value '$time' is not a number" |
126
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unless looks_like_number $time; |
127
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# For the sake of performance, we do not test the numberness of the data. |
128
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129
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# Pack args for constructor. |
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160
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436
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my @args = ( |
131
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time => $time, |
132
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populations => \@populations, |
133
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); |
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135
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160
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662
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return @args; |
136
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} |
137
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138
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around BUILDARGS => sub { |
139
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my $orig = shift; |
140
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my $class = shift; |
141
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142
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return $class->$orig(@_) if @_ != 1 or reftype $_[0]; |
143
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144
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# We have a population data line here. |
145
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my $population_data_line = shift; |
146
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my @args |
147
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= $class->_parse_population_data_line($population_data_line); |
148
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149
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return $class->$orig(@args); |
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}; |
151
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152
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# Convert this data record back to a line as found in the Treekin file. |
153
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sub stringify { |
154
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132
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132
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1
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232
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my $self = shift; |
155
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156
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# Format data like treekin C code |
157
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132
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4451
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my $self_as_string = sprintf "%22.20e ", $self->time; |
158
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$self_as_string |
159
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132
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308
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.= join q{ }, map {sprintf "%e", $_} @{ $self->_populations }; |
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1076
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5294
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132
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4319
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160
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161
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# There seems to be a trailing space in the treekin C code |
162
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# (printf "%e ") but there is none in the treekin simulator output. |
163
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# $self_as_string .= q{ }; |
164
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165
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132
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839
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return $self_as_string; |
166
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} |
167
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168
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__PACKAGE__->meta->make_immutable; |
169
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170
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171
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1; # End of Bio::RNA::Treekin::PopulationDataRecord |
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173
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__END__ |
174
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175
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176
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=pod |
177
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178
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=encoding UTF-8 |
179
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180
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=head1 NAME |
181
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182
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Bio::RNA::Treekin::PopulationDataRecord - Parse, query, and manipulate a |
183
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single data line from a I<Treekin> file. |
184
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185
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=head1 SYNOPSIS |
186
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187
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use Bio::RNA::Treekin; |
188
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189
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my $pop_data = Bio::RNA::Treekin::PopulationDataRecord->new( |
190
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'<single population data line from Treekin file>'); |
191
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192
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print "Populations at time", $pop_data->time, ":\n"; |
193
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print " min $_: ", $pop_data->of_min($_), "\n" |
194
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for 1..$pop_data->min_count; |
195
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196
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my @big_pops = grep {$pop_data->of_min($_) > 0.1} 1..$pop_data->min_count; |
197
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print 'Minima ', join(q{, }, @big_pops), ' have a population greater 0.1\n'; |
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=head1 DESCRIPTION |
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This class provides a population data record that stores the information from |
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a single data line of a I<Treekin> file. |
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=head1 METHODS |
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=head2 Bio::RNA::Treekin::PopulationDataRecord->new($treekin_file_line) |
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Construct a new population data record from a single data line of a I<Treekin> |
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file. |
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=head2 Bio::RNA::Treekin::PopulationDataRecord->new(arg => $argval, ...) |
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Construct a new population data record. |
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=over |
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=item Required arguments: |
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=over |
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=item time |
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The point in time that the population data describes. |
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=item populations |
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Array ref of the population values for all minima. |
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=back |
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=back |
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=head2 $pop_data->min_count |
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Return the number of minima in this data record. This count is not stored |
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explicitely, but inferred from the number of populations supplied during |
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construction. |
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=head2 $pop_data->time |
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Return the point in time (in arbitrary time units) that the population data |
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describes. |
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=head2 $pop_data->clone |
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Return a deep copy of this data record. |
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=head2 $pop_data->set_min_count($new_min_count) |
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Increase the number of minima to C<$new_min_count>. The newly added minima |
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will have population values of 0. |
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Currently, the number of minima cannot be decreased to avoid data loss. |
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=head2 $pop_data->populations |
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Return a list of all population values for minima 1, 2, ..., n in this ordner. |
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=head2 $pop_data->of_min($minimum) |
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Return the population value of the given C<$minimum> at the C<time> of this |
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record. |
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=head2 $pop_data->transform($maps_to_min_ref, $new_min_count) |
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Transform (reorder and resize) the population data according to a given |
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mapping (C<$maps_to_min_ref>) and resize to a given number of minima |
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(C<$new_min_count>). All minima that are not mapped to a new position are |
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discarded (replaced by zero). |
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NOTE: Ensure that no two minima are mapped to the same position or crap |
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will happen. |
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=over |
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=item Arguments: |
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=over |
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=item $maps_to_min_ref: |
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Hash ref that specifies for each kept minimum (key) to which new minimum |
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(value) it is supposed to be mapped. |
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=item $new_min_count: |
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New size (number of mins) of the record after the transformation. Defaults to |
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the maximum value of C<$maps_to_min_ref>. |
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=back |
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=back |
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=head2 $pop_data->stringify |
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=head2 "$pop_data" |
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Convert this data record into a string representation, corresponding to a |
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single line as found in a I<Treekin> file. |
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306
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=head1 AUTHOR |
307
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308
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Felix Kuehnl, C<< <felix@bioinf.uni-leipzig.de> >> |
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=head1 BUGS |
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Please report any bugs or feature requests by raising an issue at |
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L<https://github.com/xileF1337/Bio-RNA-Treekin/issues>. |
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You can also do so by mailing to C<bug-bio-rna-treekin at rt.cpan.org>, |
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or through the web interface at |
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L<https://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-RNA-Treekin>. I will be |
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notified, and then you'll automatically be notified of progress on your bug as |
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I make changes. |
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=head1 SUPPORT |
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You can find documentation for this module with the perldoc command. |
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perldoc Bio::RNA::Treekin |
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330
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You can also look for information at: |
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=over 4 |
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334
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=item * Github: the official repository |
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336
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L<https://github.com/xileF1337/Bio-RNA-Treekin> |
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=item * RT: CPAN's request tracker (report bugs here) |
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340
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L<https://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-RNA-Treekin> |
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=item * AnnoCPAN: Annotated CPAN documentation |
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L<http://annocpan.org/dist/Bio-RNA-Treekin> |
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=item * CPAN Ratings |
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L<https://cpanratings.perl.org/d/Bio-RNA-Treekin> |
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=item * Search CPAN |
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352
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L<https://metacpan.org/release/Bio-RNA-Treekin> |
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354
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=back |
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=head1 LICENSE AND COPYRIGHT |
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Copyright 2019-2021 Felix Kuehnl. |
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This program is free software: you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation, either version 3 of the License, or |
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(at your option) any later version. |
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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You should have received a copy of the GNU General Public License |
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along with this program. If not, see L<http://www.gnu.org/licenses/>. |
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375
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=cut |
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# End of Bio/RNA/Treekin/PopulationDataRecord.pm |