-
Notifications
You must be signed in to change notification settings - Fork 19
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #799 from mgcam/drop_aggregation_by_lane
Deleted aggregate_xlanes method from st::api::lims
- Loading branch information
Showing
2 changed files
with
3 additions
and
315 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -819,140 +819,6 @@ sub is_composition { | |
| return $self->rpt_list ? 1 : 0; | ||
| } | ||
|
|
||
| =head2 aggregate_xlanes | ||
| For a run-level st::api::lims object returns a list of st::api::lims | ||
| objects representing aggregated entities. | ||
| Aggregation is performed across all lanes of the lims object, unless | ||
| an explicit list of positions is gived as an argument. | ||
| If all lanes are pools, agreggation is performed per tag index (plex) | ||
| and the list contains one or more objects, each one representing a tag | ||
| index (plex). An entry for tag index zero is added as well. | ||
| If lanes are libraries, aggregation of these libraries | ||
| is performed and the list contains one object. | ||
| It is possible to aggregate one lane, though practically it does not | ||
| make much sense. | ||
| List members represent compositions and have rpt_list attribute set. | ||
| my $l = st::api::lims->new(id_run => 44); | ||
| my $a = $l->aggregate_xlanes(); | ||
| my $a = $l->aggregate_xlanes(qw/2 3/); | ||
| Assuming run id 44, for two lanes representing the same pool of four tag | ||
| indexes (1, 2, 3, 4), the list members will have the following values | ||
| of the rpt_list attribute: | ||
| 44:1:0;44:2:0 | ||
| 44:1:1;44:2:1 | ||
| 44:1:2;44:2:2 | ||
| 44:1:3;44:2:3 | ||
| 44:1:4;44:2:4 | ||
| The new objects has the same driver settings as the original object. | ||
| =cut | ||
|
|
||
| sub aggregate_xlanes { | ||
| my ($self, @positions) = @_; | ||
|
|
||
| if ($self->is_composition || $self->position) { | ||
| croak 'Not run-level object'; | ||
| } | ||
|
|
||
| my $lanes_ia = $self->children_ia; | ||
|
|
||
| ##### | ||
| # If a list of positions is given, restrict the operation to | ||
| # this set of positions. | ||
| # | ||
| if (@positions) { | ||
| my $reduced = {}; | ||
| foreach my $p (@positions) { | ||
| if (!exists $lanes_ia->{$p}) { | ||
| croak sprintf 'Requested position %i does not exists in %s', | ||
| $p, | ||
| $self->to_string(); | ||
| } | ||
| $reduced->{$p} = $lanes_ia->{$p}; | ||
| } | ||
| $lanes_ia = $reduced; | ||
| } | ||
|
|
||
| my @lanes = sort { $a->position <=> $b->position } values %{$lanes_ia}; | ||
| @positions = keys %{$lanes_ia}; | ||
|
|
||
| ##### | ||
| # We cannot have a mixture of pools and libraries. | ||
| # | ||
| my @pools = grep {$_} map { $_->is_pool ? 1 : 0 } @lanes; | ||
| if (@pools != 0 && @pools != @lanes) { | ||
| croak sprintf 'Both pools and libraries in lanes %s in %s', | ||
| join(q[, ], @positions), | ||
| $self->to_string(); | ||
| } | ||
|
|
||
| ##### | ||
| # Test function. Certain attrubutes should be the same | ||
| # across all objects of the lims array (first arg.). | ||
| # | ||
| my $can_merge = sub { | ||
| my ($lims, @attrs) = @_; | ||
| for my $attr_name (@attrs) { | ||
| my @values = grep { defined $_ } map { $_->$attr_name } @{$lims}; | ||
| if (@values != @{$lims}) { | ||
| croak qq[$attr_name is not defined for one of lims objects]; | ||
| } | ||
| @values = uniq @values; | ||
| if (@values != 1) { | ||
| croak qq[$attr_name is not the same across lims objects list]; | ||
| } | ||
| } | ||
| return; | ||
| }; # End of test function | ||
|
|
||
| my $init = $self->copy_init_args(); | ||
| delete $init->{'id_run'}; | ||
|
|
||
| my $lims4compisitions = {}; | ||
| my @test_attrs = qw/sample_id library_id/; | ||
| my $lanes_rpt_list = npg_tracking::glossary::rpt->deflate_rpts(\@lanes); | ||
| my @aggregated = (); | ||
|
|
||
| if (!@pools) { | ||
| $can_merge->(\@lanes, @test_attrs); # Test consistency | ||
| push @aggregated, __PACKAGE__->new(%{$init}, rpt_list => $lanes_rpt_list); | ||
| } else { | ||
| my @sizes = uniq (map { $_->num_children } @lanes); | ||
| if (@sizes != 1) { # Test consistency | ||
| croak 'Different number of plexes in lanes'; | ||
| } | ||
|
|
||
| ##### | ||
| # The each_arrayref function is given a list of arrays of plex-level st::api::lims | ||
| # objects, each array represent all plexes in a lane. The arrays of plexes are ordered | ||
| # by tag index. The each_arrayref function returns an iterator, which on each invocation | ||
| # collates and returns a list of first, second, etc, array members in the first, second, | ||
| # etc, invocation respectively. | ||
| # | ||
| my $ea = each_arrayref map { [$_->children()] } @lanes; | ||
| while ( my @plexes = $ea->() ) { | ||
| $can_merge->(\@plexes, @test_attrs, 'tag_index'); # Test consistency | ||
| push @aggregated, __PACKAGE__->new(%{$init}, | ||
| rpt_list => npg_tracking::glossary::rpt->deflate_rpts(\@plexes)); | ||
| } | ||
| # Add object for tag zero | ||
| push @aggregated, __PACKAGE__->new(%{$init}, | ||
| rpt_list => npg_tracking::glossary::rpt->tag_zero_rpt_list($lanes_rpt_list)); | ||
| } | ||
|
|
||
| return @aggregated; | ||
| } | ||
|
|
||
| =head2 aggregate_libraries | ||
| Given a list of lane-level C<st::api::lims> objects, finds their children, | ||
|
|
@@ -1409,7 +1275,8 @@ Marina Gourtovaia E<lt>[email protected]<gt> | |
| =head1 LICENSE AND COPYRIGHT | ||
| Copyright (C) 2013,2014,2015,2016,2017,2018,2019,2020,2021,2023 Genome Research Ltd. | ||
| Copyright (C) 2013,2014,2015,2016,2017,2018,2019,2020,2021,2023,2024 | ||
| Genome Research Ltd. | ||
| This file is part of NPG. | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters