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Merge pull request #844 from mgcam/utils4refs
Created a stand alone ref. genome name parser.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,119 @@ | ||
| package npg_tracking::data::reference::util; | ||
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| use strict; | ||
| use warnings; | ||
| use English qw(-no_match_vars); | ||
| use Carp; | ||
| use Exporter qw(import); | ||
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| our @EXPORT_OK = qw(parse_reference_genome_name); | ||
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| our $VERSION = '0'; | ||
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| sub parse_reference_genome_name { | ||
| my $reference_genome = shift; | ||
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| $reference_genome or croak 'Reference genome name is not defined'; | ||
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| my ($organism, $strain, $tversion, $analysis); | ||
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| $organism = '(?<organism>\S+)\s+'; | ||
| $strain = '(?<strain>\S+)'; | ||
| $tversion = '(?:\s+\+\s+(?<tversion>\S+))?'; | ||
| $analysis = '(?:\s+[[](?<analysis>\S+)[]])?'; | ||
| $reference_genome =~ qr{$organism [(] $strain $tversion [)] $analysis}smx; | ||
| $organism = $LAST_PAREN_MATCH{'organism'}; | ||
| $strain = $LAST_PAREN_MATCH{'strain'}; | ||
| $tversion = $LAST_PAREN_MATCH{'tversion'}; | ||
| $analysis = $LAST_PAREN_MATCH{'analysis'}; | ||
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| if ($organism && $strain) { | ||
| my @array = ($organism, $strain); | ||
| if ($tversion || $analysis) { | ||
| push @array, $tversion, $analysis; | ||
| } | ||
| return @array; | ||
| } | ||
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| return; # To be compatible with the existing code, it is essential to return | ||
| # an undefined value rather than an empty array. | ||
| } | ||
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| 1; | ||
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| __END__ | ||
| =head1 NAME | ||
| npg_tracking::data::reference::util | ||
| =head1 SYNOPSIS | ||
| =head1 DESCRIPTION | ||
| A collection of simple utility function in support of reference finder. | ||
| =head1 SUBROUTINES/METHODS | ||
| =head2 parse_reference_genome_name | ||
| Parses LIMs notation for reference genome, returns a list containing | ||
| an organism, strain (genome version) and, optionally, a transcriptome | ||
| version and/or a word indicating the type of analysis to be run. | ||
| Returns an undefined value if the input does not conform to the expected | ||
| pattern. Errors if the input string is undefined or empty. | ||
| use npg_tracking::data::reference::util qw(parse_reference_genome_name); | ||
| parse_reference_genome_name(q[]); # errors | ||
| parse_reference_genome_name(); # errors | ||
| my $name = 'Homo_sapiens (1000Genomes_hs37d5)'; | ||
| my @a = parse_reference_genome_name($name); | ||
| print join q[, ], @a; # prints Homo_sapiens, 1000Genomes_hs37d5 | ||
| # 'ensembl_release_75' defines the transcriptom to use | ||
| # 'star' defines an aligher to use | ||
| $name = 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_release_75) [star]'; | ||
| parse_reference_genome_name($name); | ||
| print join q[, ], @a; | ||
| # prints Homo_sapiens, 1000Genomes_hs37d5, ensembl_release_75, star | ||
| $name = 'Homo_sapiens 1000Genomes_hs37d5' | ||
| @a = parse_reference_genome_name($name); # no error, @a is undefined | ||
| =head1 DIAGNOSTICS | ||
| =head1 CONFIGURATION AND ENVIRONMENT | ||
| =head1 DEPENDENCIES | ||
| =head1 INCOMPATIBILITIES | ||
| =head1 BUGS AND LIMITATIONS | ||
| =head1 AUTHOR | ||
| Marina Gourtovaia | ||
| =head1 LICENSE AND COPYRIGHT | ||
| Copyright (C) 2024 Genome Research Ltd. | ||
| This file is part of NPG. | ||
| NPG is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
| the Free Software Foundation, either version 3 of the License, or | ||
| (at your option) any later version. | ||
| This program is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU General Public License for more details. | ||
| You should have received a copy of the GNU General Public License | ||
| along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| =cut |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| use strict; | ||
| use warnings; | ||
| use Test::More tests => 14; | ||
| use Test::Exception; | ||
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| my @imports = qw/parse_reference_genome_name/; | ||
| use_ok('npg_tracking::data::reference::util', @imports); | ||
| can_ok('npg_tracking::data::reference::util', @imports); | ||
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| throws_ok { parse_reference_genome_name() } | ||
| qr//, 'error if the input is undefined'; | ||
| throws_ok { parse_reference_genome_name(q[]) } qr//, | ||
| 'error if the input is an empty string'; | ||
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| my @ref = parse_reference_genome_name(q[Salmonella_enterica (Enteritidis_P125109)]); | ||
| is_deeply (\@ref, [qw(Salmonella_enterica Enteritidis_P125109)], | ||
| 'species and strain are returned'); | ||
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| @ref = parse_reference_genome_name( | ||
| q[Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome)] | ||
| ); | ||
| is_deeply (\@ref, ['Homo_sapiens', '1000Genomes_hs37d5', | ||
| 'ensembl_74_transcriptome', undef], | ||
| 'transcriptome ref genome parsing ok with correct format'); | ||
| @ref = parse_reference_genome_name( | ||
| q{Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome) [star} | ||
| ); | ||
| is_deeply (\@ref, ['Homo_sapiens', '1000Genomes_hs37d5', | ||
| 'ensembl_74_transcriptome', undef], | ||
| 'aligner ignored due to a missing square bracket'); | ||
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| is (join(q[|], parse_reference_genome_name( | ||
| q[Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome) [star]]) | ||
| ),'Homo_sapiens|1000Genomes_hs37d5|ensembl_74_transcriptome|star', | ||
| 'transcriptome ref genome parsing ok with aligner'); | ||
| @ref = parse_reference_genome_name(q[Homo_sapiens (1000Genomes_hs37d5) [star]]); | ||
| is_deeply (\@ref, ['Homo_sapiens', '1000Genomes_hs37d5', undef, 'star'], | ||
| 'transcriptome ref genome parsing ok with aligner and no transcriptome'); | ||
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| lives_ok { | ||
| parse_reference_genome_name(q[Salmonella_enterica Enteritidis_P125109]) | ||
| } 'incorrect string pattern does not cause an error'; | ||
| is (parse_reference_genome_name(q[Salmonella_enterica Enteritidis_P125109]), | ||
| undef, 'no brackets - wrong pattern, undefined value is returned'); | ||
| is (parse_reference_genome_name(q[Homo_sapiens (1000Genomes_hs37d5 + )]), undef, | ||
| 'missing transcriptome version - wrong pattern'); | ||
| is (parse_reference_genome_name( | ||
| q[Homo_sapiens (1000Genomes_hs37d5 ensembl_74_transcriptome)] | ||
| ), undef, 'missing transcriptome delimiter - wrong pattern'); | ||
| is (parse_reference_genome_name( | ||
| q[Homo_sapiens (1000Genomes_hs37d5 + ensembl_74_transcriptome]), undef, | ||
| 'missing bracket - wrong pattern'); | ||
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| 1; |