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Merge pull request #1406 from nuno-agostinho/fix/large-hgvs

Use `--max_sv_size` as the HGVSg region limit

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/modules/Bio/EnsEMBL/VEP/Parser/HGVS.pm

=head1 LICENSE

Copyright [2016-2023] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

   http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut


=head1 CONTACT

 Please email comments or questions to the public Ensembl
 developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

 Questions may also be sent to the Ensembl help desk at
 <http://www.ensembl.org/Help/Contact>.

=cut

# EnsEMBL module for Bio::EnsEMBL::VEP::Parser::HGVS
#
#

=head1 NAME

Bio::EnsEMBL::VEP::Parser::HGVS - HGVS list input parser

=head1 SYNOPSIS

my $parser = Bio::EnsEMBL::VEP::Parser::HGVS->new({
  config => $config,
  file   => 'hgvs.txt',
});

my $vf = $parser->next();

=head1 DESCRIPTION

HGVS format parser.

See http://varnomen.hgvs.org/ for spec.

Variants can be g. (genomic), c. (coding transcript),
n. (non-coding transcript) or p. (protein), though
since variants are transformed to genomic coordinates some p.
descriptions may fail to parse if they do not unambiguously resolve
to a genomic postion and ref/alt.

Requires a database connection to look up reference feature
locations, so not available in --offline mode.

=head1 METHODS

=cut


use strict;
use warnings;
no warnings 'recursion';

package Bio::EnsEMBL::VEP::Parser::HGVS;

use base qw(Bio::EnsEMBL::VEP::Parser);

use Bio::EnsEMBL::VEP::Utils qw(merge_arrays);
use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::IO::ListBasedParser;


=head2 new

  Arg 1      : hashref $args
               {
                 config    => Bio::EnsEMBL::VEP::Config,
                 file      => string or filehandle,
               }
  Example    : $parser = Bio::EnsEMBL::VEP::Parser::HGVS->new($args);
  Description: Create a new Bio::EnsEMBL::VEP::Parser::HGVS object.
  Returntype : Bio::EnsEMBL::VEP::Parser::HGVS
  Exceptions : throws if offline mode (--offline) enabled
  Caller     : Runner
  Status     : Stable

=cut

sub new {
  my $caller = shift;
  my $class = ref($caller) || $caller;
  
  my $self = $class->SUPER::new(@_);

  # requires db connection
  throw("ERROR: Cannot use HGVS format in offline mode") if $self->param('offline');

  $self->add_shortcuts(['ambiguous_hgvs']);

  return $self;
}


=head2 parser

  Example    : $io_parser = $parser->parser();
  Description: Get ensembl-io parser object used to read data from input.
  Returntype : Bio::EnsEMBL::IO::ListBasedParser
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub parser {
  my $self = shift;
  return $self->{parser} ||= Bio::EnsEMBL::IO::ListBasedParser->open($self->file);
}


=head2 create_VariationFeatures

  Example    : $vfs = $parser->create_VariationFeatures();
  Description: Create a VariationFeature object from the current line
               of input. 
  Returntype : arrayref of Bio::EnsEMBL::VariationFeature
  Exceptions : warns if unable to parse HGVS string
  Caller     : next()
  Status     : Stable

=cut

sub create_VariationFeatures {
  my $self = shift;

  my $parser = $self->parser;
  $parser->next();

  $self->skip_empty_lines();

  return [] unless $parser->{record};

  $self->line_number($self->line_number + 1);

  my $hgvs = $parser->get_value;

  # remove whitespace
  $hgvs =~ s/\s+//g;

  if ($hgvs =~ /(\[|\])/ ){
    $self->warning_msg("WARNING: Unable to parse HGVS notation \'$hgvs\'\n");
    return $self->create_VariationFeatures 
  }

  my $param_core_group = $self->param('core_type');
  my @core_groups = sort {($b eq $param_core_group) cmp ($a eq $param_core_group)} qw(core otherfeatures);
  
  my $vfa = $self->get_adaptor('variation', 'VariationFeature');
  my $vfs = [];
  my @errors;
  my $max_size = $self->param('max_sv_size') || 5000;

  foreach my $core_group(@core_groups) {
    next if (($hgvs =~ /NM_/ || $hgvs =~ /XM_/) && $core_group eq 'core');
    my $sa  = $self->get_adaptor($core_group, 'Slice');
    my $ta  = $self->get_adaptor($core_group, 'Transcript');

    # not all hgvs notations are supported yet, so we have to wrap it in an eval
    eval {
      if($self->{ambiguous_hgvs}) {
        $vfs = $vfa->fetch_all_possible_by_hgvs_notation(
          -hgvs               => $hgvs,
          -slice_adaptor      => $sa,
          -transcript_adaptor => $ta,
          -replace_ref        => $self->{lookup_ref} || 0,
          -max_size           => $max_size,
        );
      }
      else {
        push @$vfs, $vfa->fetch_by_hgvs_notation(
          -hgvs               => $hgvs,
          -slice_adaptor      => $sa,
          -transcript_adaptor => $ta,
          -replace_ref        => $self->{lookup_ref} || 0,
          -max_size           => $max_size,
        );
      }
    };

    # only log unique errors
    merge_arrays(\@errors, [$@]) if $@ && length($@) > 1;

    last if @$vfs;
  }

  unless(@$vfs || scalar(@errors) == 0) {
    my %known_messages_hash = ("MSG: Region requested must be smaller than $max_size" => 0);
    
    my @grep_names = grep(/^MSG:/, split(/\n/, $errors[0]));
    my @error_message = @errors;
    if (exists( $known_messages_hash{$grep_names[0]})) {
      $grep_names[0] .= ". This value can be adjusted with --max_sv_size.";
      @error_message = @grep_names;
    }
    
    $self->warning_msg("WARNING: Unable to parse HGVS notation \'$hgvs\'\n".join("\n", @error_message));
    return $self->create_VariationFeatures;
  }

  # warn if this looks like a gene
  if($hgvs =~ /\:[cnp]\./ && $hgvs !~ /^(ENS|[NX][CGMRP]\_|LRG\_)/) {
    my $hgvs_ref = (split(':', $hgvs))[0];
    $self->warning_msg(
      "WARNING: Possible invalid use of gene or protein identifier '$hgvs_ref' as HGVS reference; ".
      (
        $self->{ambiguous_hgvs} ?
        "$hgvs may resolve to multiple genomic locations" :
        "most likely transcript will be selected"
      )
    );
  }

  foreach my $vf(@$vfs) {

    # transfer to whole chromosome slice
    $vf = $vf->transfer($vf->slice->seq_region_Slice);

    # name it after the HGVS
    $vf->{variation_name} = $hgvs;

    # add chr attrib
    $vf->{chr} = $vf->slice->seq_region_name;

    $vf->{_line} = [$hgvs];
  }

  # post_process_vfs will do lookup_ref again, we've already done it
  my $prev = $self->{lookup_ref} || 0;
  $self->{lookup_ref} = 0;
  my $return = $self->post_process_vfs($vfs);
  $self->{lookup_ref} = $prev;

  return $return;
}

1;

1	=head1 LICENSE
2
3	Copyright [2016-2023] EMBL-European Bioinformatics Institute
4
5	Licensed under the Apache License, Version 2.0 (the "License");
6	you may not use this file except in compliance with the License.
7	You may obtain a copy of the License at
8
9	http://www.apache.org/licenses/LICENSE-2.0
10
11	Unless required by applicable law or agreed to in writing, software
12	distributed under the License is distributed on an "AS IS" BASIS,
13	WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
14	See the License for the specific language governing permissions and
15	limitations under the License.
16
17	=cut
18
19
20	=head1 CONTACT
21
22	Please email comments or questions to the public Ensembl
23	developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
24
25	Questions may also be sent to the Ensembl help desk at
26	<http://www.ensembl.org/Help/Contact>.
27
28	=cut
29
30	# EnsEMBL module for Bio::EnsEMBL::VEP::Parser::HGVS
31	#
32	#
33
34	=head1 NAME
35
36	Bio::EnsEMBL::VEP::Parser::HGVS - HGVS list input parser
37
38	=head1 SYNOPSIS
39
40	my $parser = Bio::EnsEMBL::VEP::Parser::HGVS->new({
41	config => $config,
42	file => 'hgvs.txt',
43	});
44
45	my $vf = $parser->next();
46
47	=head1 DESCRIPTION
48
49	HGVS format parser.
50
51	See http://varnomen.hgvs.org/ for spec.
52
53	Variants can be g. (genomic), c. (coding transcript),
54	n. (non-coding transcript) or p. (protein), though
55	since variants are transformed to genomic coordinates some p.
56	descriptions may fail to parse if they do not unambiguously resolve
57	to a genomic postion and ref/alt.
58
59	Requires a database connection to look up reference feature
60	locations, so not available in --offline mode.
61
62	=head1 METHODS
63
64	=cut
65
66
67	use strict;	220✔
68	use warnings;	220✔
69	no warnings 'recursion';	220✔
70
71	package Bio::EnsEMBL::VEP::Parser::HGVS;
72
73	use base qw(Bio::EnsEMBL::VEP::Parser);	220✔
74
75	use Bio::EnsEMBL::VEP::Utils qw(merge_arrays);	220✔
76	use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);	220✔
77	use Bio::EnsEMBL::Utils::Exception qw(throw warning);	220✔
78	use Bio::EnsEMBL::IO::ListBasedParser;	220✔
79
80
81	=head2 new
82
83	Arg 1 : hashref $args
84	{
85	config => Bio::EnsEMBL::VEP::Config,
86	file => string or filehandle,
87	}
88	Example : $parser = Bio::EnsEMBL::VEP::Parser::HGVS->new($args);
89	Description: Create a new Bio::EnsEMBL::VEP::Parser::HGVS object.
90	Returntype : Bio::EnsEMBL::VEP::Parser::HGVS
91	Exceptions : throws if offline mode (--offline) enabled
92	Caller : Runner
93	Status : Stable
94
95	=cut
96
97	sub new {
98	my $caller = shift;	120✔
99	my $class = ref($caller) \|\| $caller;	120✔
100
101	my $self = $class->SUPER::new(@_);	120✔
102
103	# requires db connection
104	throw("ERROR: Cannot use HGVS format in offline mode") if $self->param('offline');	120✔
105
106	$self->add_shortcuts(['ambiguous_hgvs']);	116✔
107
108	return $self;	116✔
109	}
110
111
112	=head2 parser
113
114	Example : $io_parser = $parser->parser();
115	Description: Get ensembl-io parser object used to read data from input.
116	Returntype : Bio::EnsEMBL::IO::ListBasedParser
117	Exceptions : none
118	Caller : general
119	Status : Stable
120
121	=cut
122
123	sub parser {
124	my $self = shift;	352✔
125	return $self->{parser} \|\|= Bio::EnsEMBL::IO::ListBasedParser->open($self->file);	352✔
126	}
127
128
129	=head2 create_VariationFeatures
130
131	Example : $vfs = $parser->create_VariationFeatures();
132	Description: Create a VariationFeature object from the current line
133	of input.
134	Returntype : arrayref of Bio::EnsEMBL::VariationFeature
135	Exceptions : warns if unable to parse HGVS string
136	Caller : next()
137	Status : Stable
138
139	=cut
140
141	sub create_VariationFeatures {
142	my $self = shift;	176✔
143
144	my $parser = $self->parser;	176✔
145	$parser->next();	176✔
146
147	$self->skip_empty_lines();	176✔
148
149	return [] unless $parser->{record};	176✔
150
151	$self->line_number($self->line_number + 1);	120✔
152
153	my $hgvs = $parser->get_value;	120✔
154
155	# remove whitespace
156	$hgvs =~ s/\s+//g;	120✔
157
158	if ($hgvs =~ /(\[\|\])/ ){	120✔
159	$self->warning_msg("WARNING: Unable to parse HGVS notation \'$hgvs\'\n");	×
160	return $self->create_VariationFeatures	×
161	}
162
163	my $param_core_group = $self->param('core_type');	120✔
164	my @core_groups = sort {($b eq $param_core_group) cmp ($a eq $param_core_group)} qw(core otherfeatures);	120✔
165
166	my $vfa = $self->get_adaptor('variation', 'VariationFeature');	120✔
167	my $vfs = [];	120✔
168	my @errors;	120✔
169	my $max_size = $self->param('max_sv_size') \|\| 5000;	120✔
170
171	foreach my $core_group(@core_groups) {	120✔
172	next if (($hgvs =~ /NM_/ \|\| $hgvs =~ /XM_/) && $core_group eq 'core');	152✔
173	my $sa = $self->get_adaptor($core_group, 'Slice');	144✔
174	my $ta = $self->get_adaptor($core_group, 'Transcript');	144✔
175
176	# not all hgvs notations are supported yet, so we have to wrap it in an eval
177	eval {	144✔
178	if($self->{ambiguous_hgvs}) {	144✔
179	$vfs = $vfa->fetch_all_possible_by_hgvs_notation(	26✔
180	-hgvs => $hgvs,
181	-slice_adaptor => $sa,
182	-transcript_adaptor => $ta,
183	-replace_ref => $self->{lookup_ref} \|\| 0,	26✔
184	-max_size => $max_size,
185	);
186	}
187	else {
188	push @$vfs, $vfa->fetch_by_hgvs_notation(	46✔
189	-hgvs => $hgvs,
190	-slice_adaptor => $sa,
191	-transcript_adaptor => $ta,
192	-replace_ref => $self->{lookup_ref} \|\| 0,	46✔
193	-max_size => $max_size,
194	);
195	}
196	};
197
198	# only log unique errors
199	merge_arrays(\@errors, [$@]) if $@ && length($@) > 1;	144✔
200
201	last if @$vfs;	144✔
202	}
203
204	unless(@$vfs \|\| scalar(@errors) == 0) {	120✔
205	my %known_messages_hash = ("MSG: Region requested must be smaller than $max_size" => 0);	12✔
206
207	my @grep_names = grep(/^MSG:/, split(/\n/, $errors[0]));	12✔
208	my @error_message = @errors;	12✔
209	if (exists( $known_messages_hash{$grep_names[0]})) {	12✔
210	$grep_names[0] .= ". This value can be adjusted with --max_sv_size.";	×
211	@error_message = @grep_names;	×
212	}
213
214	$self->warning_msg("WARNING: Unable to parse HGVS notation \'$hgvs\'\n".join("\n", @error_message));	12✔
215	return $self->create_VariationFeatures;	12✔
216	}
217
218	# warn if this looks like a gene
219	if($hgvs =~ /\:[cnp]\./ && $hgvs !~ /^(ENS\|[NX][CGMRP]\_\|LRG\_)/) {	108✔
220	my $hgvs_ref = (split(':', $hgvs))[0];	12✔
221	$self->warning_msg(	6✔
222	"WARNING: Possible invalid use of gene or protein identifier '$hgvs_ref' as HGVS reference; ".
223	(
224	$self->{ambiguous_hgvs} ?
225	"$hgvs may resolve to multiple genomic locations" :	6✔
226	"most likely transcript will be selected"
227	)
228	);
229	}
230
231	foreach my $vf(@$vfs) {	108✔
232
233	# transfer to whole chromosome slice
234	$vf = $vf->transfer($vf->slice->seq_region_Slice);	148✔
235
236	# name it after the HGVS
237	$vf->{variation_name} = $hgvs;	148✔
238
239	# add chr attrib
240	$vf->{chr} = $vf->slice->seq_region_name;	148✔
241
242	$vf->{_line} = [$hgvs];	148✔
243	}
244
245	# post_process_vfs will do lookup_ref again, we've already done it
246	my $prev = $self->{lookup_ref} \|\| 0;	108✔
247	$self->{lookup_ref} = 0;	108✔
248	my $return = $self->post_process_vfs($vfs);	108✔
249	$self->{lookup_ref} = $prev;	108✔
250
251	return $return;	108✔
252	}
253
254	1;

Ensembl / ensembl-vep / 3246

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