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Commit 564cf93b authored by Matthew Laird's avatar Matthew Laird
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Fixes: 

- Removed redundant code for calling _process_subseq()
- Fixed calculation error when translating from genomic space to protein space
- Added tests for single bp regions, both in direct sequences and translated sequence
parent 0915987d
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1 merge request!91ENSCORESW-1480
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lib/EnsEMBL/REST/Controller/Sequence.pm
+ 28
− 24
View file @ 564cf93b
......@@ -156,6 +156,13 @@ sub _process {
Catalyst::Exception->throw(qq{The type '$type' is not understood by this service}) unless $allowed_values{type}{$type};
if($c->request->param('start') || $c->request->param('end')) {
# We don't support circular features at this time, if it's a circular
# feature, and not a translation, throw an error.
unless($object->isa('Bio::EnsEMBL::Translation')) {
my $feat_slice = $object->feature_Slice();
Catalyst::Exception->throw(qq{Circular slices aren't supported for sequence trimming at this time}) if($feat_slice->is_circular());
}
# It doesn't make sense to expand the sequence when doing a sub-sequence
if($c->request->param('expand_5prime') || $c->request->param('expand_3prime')) {
Catalyst::Exception->throw(qq{You may not expand the 3prime or 5prime sequence end when requesting a sub-sequence});
......@@ -203,42 +210,33 @@ sub _process_feature {
if($object->isa('Bio::EnsEMBL::Translation')) {
$molecule = 'protein';
$seq = $object->transcript()->translate()->seq();
# Grab the subsequence if we've been asked to trim the ends
$seq = $self->_process_subseq($c, $seq) if($c->stash()->{dosubseq});
}
#Transcripts
elsif($object->isa('Bio::EnsEMBL::PredictionTranscript')) {
if($type eq 'cdna') {
$seq = $object->spliced_seq($mask_feature);
# Grab the subsequence if we've been asked to trim the ends
$seq = $self->_process_subseq($c, $seq) if($c->stash()->{dosubseq});
}
elsif($type eq 'cds') {
$seq = $object->translateable_seq();
# Grab the subsequence if we've been asked to trim the ends
$seq = $self->_process_subseq($c, $seq) if($c->stash()->{dosubseq});
}
elsif($type eq 'protein') {
$molecule = 'protein';
$seq = $object->translate()->seq();
if($c->stash()->{dosubseq}) {
# It's a protein that's been requested so we have to translate
# the coordinates first
$self->_translate_coordinates($c, $object);
$seq = $self->_process_subseq($c, $seq);
}
# It's a protein that's been requested so we have to translate
# the coordinates first
$self->_translate_coordinates($c, $object) if($c->stash()->{dosubseq});
}
}
elsif($object->isa('Bio::EnsEMBL::Transcript')) {
if($type eq 'cdna') {
$seq = $object->spliced_seq($mask_feature);
$seq = $self->_process_subseq($c, $seq) if($c->stash()->{dosubseq});
}
elsif($type eq 'cds') {
$seq = $object->translateable_seq();
# We might not have a translatable sequence, be sure
# we do before attempting to trim
$seq = $self->_process_subseq($c, $seq) if($c->stash()->{dosubseq} && $seq);
}
#If protein perform recursive calls with the Translation object
elsif($type eq 'protein') {
......@@ -251,6 +249,7 @@ sub _process_feature {
foreach my $t (@translations) {
# Catch case where no translation is available for a transcript
next unless $t;
push(@sequences, @{$self->_process_feature($c, $t, $type)});
}
}
......@@ -297,6 +296,10 @@ sub _process_feature {
}
if($seq) {
# Grab the subsequence if we've been asked to trim the ends
$seq = $self->_process_subseq($c, $seq) if($c->stash()->{dosubseq});
push(@sequences, {
id => $object->stable_id(),
seq => $seq,
......@@ -338,9 +341,11 @@ sub _check_limits {
if($start < 0 || $start > $seq_len) {
Catalyst::Exception->throw(qq{Your start coordinate is not within the sequence requested})
}
if($end < 1 || $end > $seq_len + 1) {
Catalyst::Exception->throw(qq{Your end coordinate is not within the sequence requested})
}
if($start > $end) {
Catalyst::Exception->throw(qq{Your start coordinate cannot be larger than your end})
}
......@@ -355,9 +360,11 @@ sub _translate_coordinates {
my ($self, $c, $obj) = @_;
# Return if we've already translated the coordinates
return if($c->{stash}->{coordstranslated});
return if($c->stash->{coordstranslated});
# Do we have a translation?
return unless($obj->translate());
my $seq_len = length $obj->spliced_seq();
my $start; my $end;
if($obj->strand() == 1) {
$start = $c->request->param('start') ? $c->request->param('start') + $obj->seq_region_start() - 1 : $obj->seq_region_start();
......@@ -366,12 +373,9 @@ sub _translate_coordinates {
# Things get a little messy if we're on the reverse strand, we have to count from
# opposite ends.
$end = $c->request->param('start') ? $obj->seq_region_end() - $c->request->param('start') : $obj->seq_region_end();
$start = $c->request->param('end') ? $obj->seq_region_start() + $seq_len - $c->request->param('end') : $obj->seq_region_start();
$start = $c->request->param('end') ? $obj->seq_region_end() - $c->request->param('end') : $obj->seq_region_start();
}
# Do we have a translation?
return unless($obj->translate());
my $transcript_mapper = $obj->get_TranscriptMapper();
# Grab the coordinates for the peptide sequence that maps from
......@@ -398,7 +402,7 @@ sub _translate_coordinates {
}
# Remember we've translated the coordinates so we don't try again
$c->{stash}->{coordstranslated} = 1;
$c->stash->{coordstranslated} = 1;
}
# For the fustrating flow where you're going from a Gene and are outputting
......@@ -408,17 +412,17 @@ sub _translate_coordinates {
sub _push_start_end {
my ($self, $c) = @_;
$c->{stash}->{orig_start} = $c->request->param('start') if($c->request->param('start'));
$c->{stash}->{orig_end} = $c->request->param('end') if($c->request->param('end'));
$c->stash->{orig_start} = $c->request->param('start') if($c->request->param('start'));
$c->stash->{orig_end} = $c->request->param('end') if($c->request->param('end'));
}
sub _pop_start_end {
my ($self, $c) = @_;
$c->request->params->{'start'} = $c->{stash}->{orig_start} if($c->{stash}->{orig_start});
$c->request->params->{'end'} = $c->{stash}->{orig_end} if($c->{stash}->{orig_end});
$c->request->params->{'start'} = $c->stash->{orig_start} ? $c->stash->{orig_start} : undef;
$c->request->params->{'end'} = $c->stash->{orig_end} ? $c->stash->{orig_end} : undef;
$c->{stash}->{coordstranslated} = 0;
$c->stash->{coordstranslated} = 0;
}
sub _enrich_slice {
......
t/sequences.t
+ 34
− 12
View file @ 564cf93b
......@@ -316,12 +316,22 @@ FASTA
{
my $id = 'ENSP00000259806';
my $url = "/sequence/id/$id?type=protein&start=10&end=30";
my $fasta = fasta_GET($url, 'Getting protein sub-sequence from transcript without end parameter');
my $fasta = fasta_GET($url, 'Getting protein sub-sequence from translation feature with start and end');
my $expected = <<'FASTA';
>ENSP00000259806
APLRRACSPVPGALQAALMSP
FASTA
is($fasta, $expected, 'Getting protein sub-sequence from transcript without end parameter');
is($fasta, $expected, 'Getting protein sub-sequence from translation feature with start and end');
}
{
my $id = 'ENSP00000259806';
my $url = "/sequence/id/$id?type=protein&start=30&end=30";
my $fasta = fasta_GET($url, 'Getting single bp protein sub-sequence from translation feature');
my $expected = <<'FASTA';
>ENSP00000259806
P
FASTA
is($fasta, $expected, 'Getting single bp sub-sequence from translation feature');
}
{
my $id = 'ENST00000400701';
......@@ -329,25 +339,37 @@ FASTA
my $fasta = fasta_GET($url, 'Getting protein sub-sequence from transcript without start parameter');
my $expected = <<'FASTA';
>ENSP00000383537
XSNLKRDVAHLYRGVGSRYIMGSGESFMQLQQRLLREKEAKIRKALDRLRKKRHLLRRQR
TRREFPVISVVGYTNCGKTTLIKALTGDAAIQPRDQLFATLDVTAHAGTLPSRMTVLYVD
TIGFLSQLPHGLIESFSATLEDVAHSDLILHVRDVSHPEAELQKCSVLSTLRGLQLPAPL
LDSMVEVHNKVDLVPGYSPTEPNVVPVSALRGHGLQELKAELDAAVLKATGRQILTLRVR
LAGAQLS
XSNLKRDVAHLYRGVGSRYIMGSG
FASTA
is($fasta, $expected, 'Getting protein sub-sequence from transcript without start parameter');
}
{
my $id = 'ENST00000400701';
my $url = "/sequence/id/$id?type=protein&start=10&end=10";
my $fasta = fasta_GET($url, 'Getting protein sub-sequence from transcript with length 1bp');
my $expected = <<'FASTA';
>ENSP00000383537
K
FASTA
is($fasta, $expected, 'Getting protein sub-sequence from transcript with length 1bp');
}
{
my $id = 'ENSG00000112699';
my $url = "/sequence/id/$id?type=protein&multiple_sequences=1&start=300000";
my $url = "/sequence/id/$id?type=protein&multiple_sequences=1&start=150000";
my $fasta = fasta_GET($url, 'Getting protein sub-sequence from gene, using multiple');
my $expected = <<'FASTA';
>ENSP00000436726
AMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHV
TVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTNPNA
ISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYP
RSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQL
ECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKT
IVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELV
REMVHADVELMRTNPNA
>ENSP00000370194
GANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIA
TGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEV
ISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYP
RSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQL
ECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKT
IVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELV
REMVHADVELMRTNPNA
FASTA
is($fasta, $expected, 'Getting protein sub-sequence from gene, using multiple');
}
......
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