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Merge pull request #765 from mgcam/lims_drop_inline_index
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Deleted the code for inline indexes.
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@dozy
dozy authored Oct 30, 2023
2 parents 928d753 + a246c44 commit 322a40a
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Showing 2 changed files with 84 additions and 246 deletions.
326 changes: 81 additions & 245 deletions lib/st/api/lims.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -203,6 +203,7 @@ sub BUILD {
Readonly::Hash my %ATTRIBUTE_LIST_METHODS => {
'library' => [qw/ id
name
type
/],
'sample' => [qw/ accession_number
cohort
Expand All @@ -220,6 +221,68 @@ Readonly::Hash my %ATTRIBUTE_LIST_METHODS => {
/]
};

=head2 library_names
A list of library names. if $self->is_pool is true, returns unique library
names of plex-level objects, otherwise returns object's own library name.
Takes an optional argument with_spiked_control, wich defaults to true.
=head2 library_ids
Similar to library_names, but for ids.
=head2 library_types
Similar to library_names, but for types.
=head2 sample_names
A list of sample names. if $self->is_pool is true, returns unique sample
names of plex-level objects, otherwise returns object's own sample name.
Takes an optional argument with_spiked_control, wich defaults to true.
=head2 sample_cohorts
Similar to sample_names, but for cohorts.
=head2 sample_donor_ids
Similar to sample_names, but for donor_ids.
=head2 sample_ids
Similar to sample_names, but for ids.
=head2 sample_public_names
Similar to sample_names, but for public_names.
=head2 sample_supplier_names
Similar to sample_names, but for supplier_names.
=head2 study_names
A list of study names. if $self->is_pool is true, returns unique study
names of plex-level objects, otherwise returns object's own study name.
Takes an optional argument with_spiked_control, wich defaults to true.
=head2 study_accession_numbers
Similar to study_names, but for accession_numbers.
=head2 study_ids
Similar to study_names, but for ids.
=head2 study_titles
Similar to study_names, but for study_titles.
=cut

# Dynamicaly generate methods for getting 'plural' values.
# The methods are documented above.
foreach my $object_type (keys %ATTRIBUTE_LIST_METHODS) {
foreach my $property (@{$ATTRIBUTE_LIST_METHODS{$object_type}}) {
my $attr_name = join q[_], $object_type, $property;
Expand Down Expand Up @@ -316,90 +379,6 @@ for my $m ( @METHODS ){
# All methods are created, now aliases for methods can be defined.
alias primer_panel => 'gbs_plex_name';

=head2 inline_index_read
index read
=cut

has 'inline_index_read' => (isa => 'Maybe[Int]',
is => 'ro',
init_arg => undef,
lazy_build => 1,
);

sub _build_inline_index_read {
my $self = shift;
my @x = _parse_sample_description($self->_sample_description);
return $x[3]; ## no critic (ProhibitMagicNumbers)
}

has 'inline_index_end' => (isa => 'Maybe[Int]',
is => 'ro',
init_arg => undef,
lazy_build => 1,
);

=head2 inline_index_end
index end
=cut

sub _build_inline_index_end {
my $self = shift;
my @x = _parse_sample_description($self->_sample_description);
return $x[2];
}

=head2 inline_index_start
index start
=cut

has 'inline_index_start' => (isa => 'Maybe[Int]',
is => 'ro',
init_arg => undef,
lazy_build => 1,
);

sub _build_inline_index_start {
my $self = shift;
my @x = _parse_sample_description($self->_sample_description);
return $x[1];
}

=head2 inline_index_exists
=cut

has 'inline_index_exists' => (isa => 'Bool',
is => 'ro',
init_arg => undef,
lazy_build => 1,
);

sub _build_inline_index_exists {
my $self = shift;
return _tag_sequence_from_sample_description($self->_sample_description) ? 1 : 0;
}

has '_sample_description' => (isa => 'Maybe[Str]',
is => 'ro',
init_arg => undef,
lazy_build => 1,
);

sub _build__sample_description {
my $self = shift;
return $self->sample_description if ($self->sample_description);
foreach my $c ($self->children) {
return $c->sample_description if ($c->sample_description);
}
return;
}

=head2 is_phix_spike
True for a plex library that is the spiked phiX.
Expand Down Expand Up @@ -441,9 +420,6 @@ sub _build_tag_sequence {
Read-only array accessor, not possible to set from the constructor.
Empty array on a lane level and for zero tag_index.
Might return not the index given by LIMs, but the one contained in the
sample description.
If dual index is used, the array contains two sequences. The secons index
might come from LIMS or, if LIMs has one long index, it will be split in two.
Expand All @@ -456,34 +432,24 @@ has 'tag_sequences' => (isa => 'ArrayRef',
sub _build_tag_sequences {
my $self = shift;

my ($seq, $seq2);
my @sqs = ();

if ($self->tag_index) {
if (!$self->spiked_phix_tag_index || $self->tag_index != $self->spiked_phix_tag_index) {
if ($self->sample_description) {
$seq = _tag_sequence_from_sample_description($self->sample_description);
my $seq = $self->default_tag_sequence;
if ($seq) {
push @sqs, $seq;
$seq = $self->default_tagtwo_sequence;
if ($seq) {
push @sqs, $seq;
}
}
if (!$seq) {
$seq = $self->default_tag_sequence;
if ($seq && $self->default_tagtwo_sequence) {
$seq2 = $self->default_tagtwo_sequence;
}
}
}

my @sqs = ();
if ($seq) {
push @sqs, $seq;
}
if ($seq2) {
push @sqs, $seq2;
}

if (scalar @sqs == 1) {
if (length($sqs[0]) == $DUAL_INDEX_TAG_LENGTH) {
my $tag_length = $DUAL_INDEX_TAG_LENGTH/2;
push @sqs, substr $sqs[0], $tag_length;
$sqs[0] = substr $sqs[0], 0, $tag_length;
if (scalar @sqs == 1) {
if (length($sqs[0]) == $DUAL_INDEX_TAG_LENGTH) {
my $tag_length = $DUAL_INDEX_TAG_LENGTH/2;
push @sqs, substr $sqs[0], $tag_length;
$sqs[0] = substr $sqs[0], 0, $tag_length;
}
}
}

Expand Down Expand Up @@ -1083,96 +1049,6 @@ sub _single_attribute {
return;
}

=head2 library_names
A list of library names. if $self->is_pool is true, returns unique library
names of plex-level objects, otherwise returns object's own library name.
Takes an optional argument with_spiked_control, wich defaults to true.
=cut

=head2 library_ids
Similar to library_names, but for ids.
=cut


=head2 sample_names
A list of sample names. if $self->is_pool is true, returns unique sample
names of plex-level objects, otherwise returns object's own sample name.
Takes an optional argument with_spiked_control, wich defaults to true.
=cut


=head2 sample_cohorts
Similar to sample_names, but for cohorts.
=cut


=head2 sample_donor_ids
Similar to sample_names, but for donor_ids.
=cut


=head2 sample_ids
Similar to sample_names, but for ids.
=cut


=head2 sample_public_names
Similar to sample_names, but for public_names.
=cut


=head2 sample_supplier_names
Similar to sample_names, but for supplier_names.
=cut


=head2 study_names
A list of study names. if $self->is_pool is true, returns unique study
names of plex-level objects, otherwise returns object's own study name.
Takes an optional argument with_spiked_control, wich defaults to true.
=cut


=head2 study_accession_numbers
Similar to study_names, but for accession_numbers.
=cut


=head2 study_ids
Similar to study_names, but for ids.
=cut


=head2 study_titles
Similar to study_names, but for study_titles.
=cut


=head2 library_type
Read-only accessor, not possible to set from the constructor.
Expand All @@ -1185,54 +1061,14 @@ has 'library_type' => (isa => 'Maybe[Str]',
);
sub _build_library_type {
my $self = shift;
if($self->is_pool) { return; }
return _derived_library_type($self);
}

sub _derived_library_type {
my $o = shift;
my $type = $o->default_library_type;
if ($o->tag_index && $o->sample_description &&
_tag_sequence_from_sample_description($o->sample_description)) {
$type = '3 prime poly-A pulldown';
my $type;
if (!$self->is_pool) {
$type = $self->default_library_type;
}
$type ||= undef;
return $type;
}

sub _tag_sequence_from_sample_description {
my $desc = shift;
my @x = _parse_sample_description($desc);
return $x[0];
}

sub _parse_sample_description {
my $desc = shift;
my $tag=undef;
my $start=undef;
my $end=undef;
my $read=undef;
if ($desc && (($desc =~ m/base\ indexing\ sequence/ismx) && ($desc =~ m/enriched\ mRNA/ismx))) {
($tag) = $desc =~ /\(([ACGT]+)\)/smx;
if ($desc =~ /bases\ (\d+)\ to\ (\d+)\ of\ read\ 1/smx) {
($start, $end, $read) = ($1, $2, 1);
} elsif ($desc =~ /bases\ (\d+)\ to\ (\d+)\ of\ non\-index\ read\ (\d)/smx) {
($start, $end, $read) = ($1, $2, $3);
} else {
croak q[Error parsing sample description ] . $desc;
}
}
return ($tag, $start, $end, $read);
}

=head2 library_types
A list of library types, excluding spiked phix library
=cut
sub library_types {
my ($self) = @_;
return $self->_list_of_attributes('_derived_library_type',0);
return $type;
}

=head2 driver_method_list
Expand Down
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