From 04bdd5c1b8e814a7fbab715672b07c06ffc0dc71 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Tue, 20 Mar 2012 14:41:58 +0000
Subject: [PATCH] Split the parsing of a location string away from the use case
---
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 84 ++++++++++++++++-------
1 file changed, 60 insertions(+), 24 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index b78c3d362e..1809db2068 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -470,17 +470,68 @@ sub fetch_by_region {
sub fetch_by_toplevel_location {
my ($self, $location, $no_warnings) = @_;
- throw 'You must specify a location' if ! $location;
+ my ($seq_region_name, $start, $end, $strand) = $self->parse_location_to_values($location, $no_warnings);
+
+ if(! $seq_region_name) {
+ return;
+ }
+
+ if(defined $start && defined $end && $start > $end) {
+ throw "Cannot request a slice whose start is greater than its end. Start: $start. End: $end";
+ }
+
+ my $coord_system_name = 'toplevel';
+ my $slice = $self->fetch_by_region($coord_system_name, $seq_region_name, $start, $end, $strand, undef, 0);
+ return unless $slice;
+
+ my $srl = $slice->seq_region_length();
+ my $name = $slice->seq_region_name();
+ if(defined $start && $start > $srl) {
+ throw "Cannot request a slice whose start ($start) is greater than $srl for $name.";
+ }
+ if(defined $end && $end > $srl) {
+ warning "Requested end ($end) is greater than $srl for $name. Resetting to $srl" if ! $no_warnings;
+ $slice->{end} = $srl;
+ }
+
+ return $slice;
+}
+
+=head2 parse_location_to_values
+
+ Arg [1] : string $location
+ Ensembl formatted location. Can be a format like
+ C<name:start-end>, C<name:start..end>, C<name:start:end>,
+ C<name:start>, C<name>. We can also support strand
+ specification as a +/- or 1/-1.
+
+ Location names must be separated by a C<:>. All others can be
+ separated by C<..>, C<:> or C<->.
+ Arg[2] : boolean $no_warnings
+ Suppress warnings from this method
+ Example : my ($name, $start, $end, $strand) = $sa->parse_location_to_values('X:1..100:1);
+ Description : Takes in an Ensembl location String and returns the parsed
+ values
+ Returntype : List. Contains name, start, end and strand
+
+=cut
+
+
+sub parse_location_to_values {
+ my ($self, $location, $no_warnings) = @_;
+
+ throw 'You must specify a location' if ! $location;
+
#cleanup any nomenclature like 1_000 or 1 000 or 1,000
my $number_seps_regex = qr/\s+|,|_/;
- my $separator = qr/(?:-|[.]{2}|\:)?/;
- my $number = qr/[0-9,_ E]+/xms;
- my $strand = qr/[+-1]|-1/xms;
+ my $separator_regex = qr/(?:-|[.]{2}|\:)?/;
+ my $number_regex = qr/[0-9,_ E]+/xms;
+ my $strand_regex = qr/[+-1]|-1/xms;
- my $regex = qr/^(\w+) \s* :? \s* ($number)? $separator ($number)? $separator ($strand)? $/xms;
-
- if(my ($seq_region_name, $start, $end, $strand) = $location =~ $regex) {
+ my $regex = qr/^(\w+) \s* :? \s* ($number_regex)? $separator_regex ($number_regex)? $separator_regex ($strand_regex)? $/xms;
+ my ($seq_region_name, $start, $end, $strand);
+ if(($seq_region_name, $start, $end, $strand) = $location =~ $regex) {
if(defined $strand) {
if(!looks_like_number($strand)) {
@@ -505,24 +556,9 @@ sub fetch_by_toplevel_location {
if(defined $start && defined $end && $start > $end) {
throw "Cannot request a slice whose start is greater than its end. Start: $start. End: $end";
}
-
- my $coord_system_name = 'toplevel';
- my $slice = $self->fetch_by_region($coord_system_name, $seq_region_name, $start, $end, $strand, undef, 0);
- return unless $slice;
-
- my $srl = $slice->seq_region_length();
- my $name = $slice->seq_region_name();
- if(defined $start && $start > $srl) {
- throw "Cannot request a slice whose start ($start) is greater than $srl for $name.";
- }
- if(defined $end && $end > $srl) {
- warning "Requested end ($end) is greater than $srl for $name. Resetting to $srl" if ! $no_warnings;
- $slice->{end} = $srl;
- }
-
- return $slice;
}
- return;
+
+ return ($seq_region_name, $start, $end, $strand);
}
=head2 fetch_by_region_unique
--
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