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Remove redundant symbolic alt to so term hash #1075

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Remove redundant symbolic alt to so term hash #1075

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e9dbd08
Remove redundant symbolic alt to so term hash
nakib103 Mar 21, 2024
842e47b
Add TREP
nakib103 May 22, 2024
bfeeea9
Generalize SO term hash name
nakib103 May 22, 2024
717ebbd
Added logic to interpret abbrv to VEP defined symbol
nakib103 May 22, 2024
711122a
Fix regex assignment
nakib103 May 22, 2024
5b8d16f
Fix typos
nakib103 May 22, 2024
2a12d39
Avoid circular reference
nakib103 May 23, 2024
cf25c68
Send empty hash for first arg of get_SO_term
nakib103 Aug 20, 2024
c26142e
Merge branch 'main' into fix_sv_so
nakib103 Aug 20, 2024
a588067
Add ensembl-vep cloning in travis
nakib103 Aug 20, 2024
2ab4ead
Add ensembl-vep to the path
nakib103 Aug 20, 2024
d252984
Add relevant ensembl-vep branch to check UT
nakib103 Aug 21, 2024
a333f87
Revert back the changes in travis
nakib103 Aug 21, 2024
014c518
Use undef instead of empty hash
nakib103 Sep 26, 2024
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1 change: 1 addition & 0 deletions .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@ before_install:
- git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl.git
- git clone --branch main --depth 1 https://github.com/Ensembl/ensembl-hive.git
- git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl-io.git
- git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl-vep.git
- git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl-funcgen.git
- git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
- git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
Expand Down
25 changes: 25 additions & 0 deletions modules/Bio/EnsEMBL/Variation/Utils/Config.pm
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Expand Up @@ -31,6 +31,7 @@ our @EXPORT_OK = qw(
$OVERLAP_CONSEQUENCE_CLASS
$MAX_ATTRIB_CODE_LENGTH
%SO_ACC_MAPPER
%SO_TERMS
);

our $OVERLAP_CONSEQUENCE_CLASS = 'Bio::EnsEMBL::Variation::OverlapConsequence';
Expand Down Expand Up @@ -1382,5 +1383,29 @@ our %SO_ACC_MAPPER = (
}
);

# Used to convert symbolic alternative allele to SO term
our %SO_TERMS = (
INS => 'insertion',
INS_ME => 'mobile_element_insertion',
INS_ALU => 'Alu_insertion',
INS_HERV => 'HERV_insertion',
INS_LINE1 => 'LINE1_insertion',
INS_SVA => 'SVA_insertion',

DEL => 'deletion',
DEL_ME => 'mobile_element_deletion',
DEL_ALU => 'Alu_deletion',
DEL_HERV => 'HERV_deletion',
DEL_LINE1 => 'LINE1_deletion',
DEL_SVA => 'SVA_deletion',

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TREP => 'tandem_repeat',
TDUP => 'tandem_duplication',
DUP => 'duplication',
CNV => 'copy_number_variation',
INV => 'inversion',
BND => 'chromosome_breakpoint'
);


1;
98 changes: 13 additions & 85 deletions modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
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Expand Up @@ -86,11 +86,13 @@ use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor;
use Bio::EnsEMBL::Variation::Utils::VariationEffect qw(overlap);
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Variation::Utils::Sequence qw(unambiguity_code SO_variation_class);
use Bio::EnsEMBL::Variation::Utils::Config qw(%SO_TERMS);
use Bio::EnsEMBL::Variation::Utils::EnsEMBL2GFF3;
use Bio::EnsEMBL::Variation::StructuralVariationFeature;
use Bio::EnsEMBL::Variation::DBSQL::StructuralVariationFeatureAdaptor;
use Bio::EnsEMBL::Variation::TranscriptStructuralVariation;
use Bio::EnsEMBL::Variation::Source;
use Bio::EnsEMBL::VEP::Parser qw(get_SO_term &check_format);

# we need to manually include all these modules for caching to work
use Bio::EnsEMBL::CoordSystem;
Expand All @@ -113,8 +115,6 @@ use vars qw(@ISA @EXPORT_OK);
@ISA = qw(Exporter);

@EXPORT_OK = qw(
&_valid_region_regex
&check_format
&detect_format
&parse_line
&vf_to_consequences
Expand Down Expand Up @@ -384,68 +384,6 @@ sub parse_line {
return $vfs;
}

sub _valid_region_regex {
return qr/^([^:]+):(\d+)-(\d+)(:[-\+]?1)?[\/:]([a-z0-9:]{3,}|[ACGTN-]+)$/i;
}

# sub-routine to check format of string
sub check_format {
my @line = @_;
my $format;

# any changes here must be copied to the JavaScript file to run instant VEP:
# public-plugins/tools/htdocs/components/20_VEPForm.js

# region: chr21:10-10:1/A
if ( scalar @line == 1 && $line[0] =~ &_valid_region_regex() ) {
$format = 'region';
}

# SPDI: NC_000016.10:68684738:G:A
elsif ( scalar @line == 1 && $line[0] =~ /^(.*?\:){2}([^\:]+|)$/i ) {
$format = 'spdi';
}

# CAID: CA9985736
elsif ( scalar @line == 1 && $line[0] =~ /^CA\d{1,}$/i ) {
$format = 'caid';
}

# HGVS: ENST00000285667.3:c.1047_1048insC
elsif (
scalar @line == 1 &&
$line[0] =~ /^([^\:]+)\:.*?([cgmrp]?)\.?([\*\-0-9]+.*)$/i
) {
$format = 'hgvs';
}

# variant identifier: rs123456
elsif ( scalar @line == 1 ) {
$format = 'id';
}

# VCF: 20 14370 rs6054257 G A 29 0 NS=58;DP=258;AF=0.786;DB;H2 GT:GQ:DP:HQ
elsif (
$line[0] =~ /(chr)?\w+/ &&
$line[1] =~ /^\d+$/ &&
exists $line[3] && $line[3] =~ /^[ACGTN\-\.]+$/i &&
exists $line[4]
) {
$format = 'vcf';
}

# ensembl: 20 14370 14370 A/G +
elsif (
$line[0] =~ /\w+/ &&
$line[1] =~ /^\d+$/ &&
exists $line[2] && $line[2] =~ /^\d+$/ &&
exists $line[3] && $line[3] =~ /([a-z]{2,})|([ACGTN-]+\/[ACGTN-]+)/i
) {
$format = 'ensembl';
}
return $format;
}

# sub-routine to detect format of input
sub detect_format {
my $line = shift;
Expand Down Expand Up @@ -478,12 +416,7 @@ sub parse_ensembl {
my $so_term;

# convert to SO term
my %terms = (
INS => 'insertion',
DEL => 'deletion',
TDUP => 'tandem_duplication',
DUP => 'duplication'
);
my %terms = %SO_TERMS;

$so_term = defined $terms{$allele_string} ? $terms{$allele_string} : $allele_string;

Expand Down Expand Up @@ -631,14 +564,7 @@ sub parse_vcf {

if(defined($type)) {
# convert to SO term
my %terms = (
INS => 'insertion',
DEL => 'deletion',
TDUP => 'tandem_duplication',
DUP => 'duplication'
);

$so_term = defined $terms{$type} ? $terms{$type} : $type;
$so_term = get_SO_term(undef, $type) || $type;
}

my $svf = Bio::EnsEMBL::Variation::StructuralVariationFeature->new_fast({
Expand Down Expand Up @@ -933,14 +859,16 @@ sub convert_to_vcf {
else {

# convert to SO term
my %terms = (
'insertion' => 'INS',
'deletion' => 'DEL',
'tandem_duplication' => 'TDUP',
'duplication' => 'DUP'
);
my %terms = reverse %SO_TERMS;
my $abbrev = $terms{$vf->class_SO_term} || $vf->class_SO_term;

$abbrev = "DUP:TANDEM" if $abbrev eq "TDUP";
$abbrev = "CNV:TR" if $abbrev eq "TREP";
$abbrev =~ s/_/:/ if $abbrev =~ /^(INS|DEL)_ME$/;
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This is correct as of now, but is not future-proof in case other INS/DEL subtypes are supported in the future. Maybe we could change the INS/DEL to contain the ME, such as INS_ME_ALU instead of INS_ALU to be more precise.

This is a bit nitpick-y so maybe just ignore this comment. 😛

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Noted! but I think that requires a bigger change and not within the scope/objective of this PR.

$abbrev =~ s/_/:ME:/ if $abbrev =~ /^(INS|DEL)_[A-Z0-9]+$/;

my $alt = '<'.($terms{$vf->class_SO_term} || $vf->class_SO_term).'>';
my $alt = '<'.$abbrev.'>';
$alt = ( split(/\//, $vf->allele_string, 2) )[1] if ($alt eq "BND");

return [
$vf->{chr} || $vf->seq_region_name,
Expand Down
2 changes: 1 addition & 1 deletion travisci/harness.sh
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/bin/bash

export PERL5LIB=$PWD/bioperl-live:$PWD/ensembl-test/modules:$PWD/ensembl/modules:$PWD/ensembl-hive/modules:$PWD/modules:$PWD/scripts/import/:$PWD/ensembl-io/modules:$PWD/ensembl-funcgen/modules
export PERL5LIB=$PWD/bioperl-live:$PWD/ensembl-test/modules:$PWD/ensembl/modules:$PWD/ensembl-hive/modules:$PWD/modules:$PWD/scripts/import/:$PWD/ensembl-io/modules:$PWD/ensembl-vep/modules:$PWD/ensembl-funcgen/modules

export PATH=$PATH:$PWD/C_code:$PWD/htslib

Expand Down