package MS::CV; use strict; use warnings; use Carp; use Exporter qw/import/; use File::ShareDir qw/dist_file/; use Storable; my $terms; my %exports; my %roots; our %EXPORT_TAGS; our @EXPORT_OK; BEGIN { # read in ontology file my $fn_obo = dist_file('MS' => 'cv.stor'); $terms = retrieve $fn_obo; # necessary for symbol table manipulation no strict 'refs'; # generate constants and track root terms for my $id (keys %{$terms} ) { my $ref = $terms->{$id}; my $const_name = $ref->{constant} ; next if (! defined $const_name); my $cv = $ref->{cv}; die "name undefined for $id" if (! defined $const_name); # define constant *$const_name = sub () {$id}; push @{ $exports{$cv} }, $const_name; push @MS::CV::EXPORT_OK, $const_name; push @{$roots{$cv} }, $id if (! exists $ref->{is_a}); } use strict 'refs'; # update exportable constants and functions %MS::CV::EXPORT_TAGS = map {$_ => \@{ $exports{$_} }} keys %exports; push @MS::CV::EXPORT_OK, qw/is_a print_tree units_for regex_for cv_name/; } # end BEGIN sub cv_name { return $terms->{$_[0]}->{name}; } sub is_a { my ($child, $parent) = @_; return undef if (! defined $terms->{$child}); return 0 if (! defined $terms->{$child}->{is_a}); my @parents = @{ $terms->{$child}->{is_a} }; my $retval = 0; for (@parents) { return 1 if ($_ eq $parent); $retval += is_a( $_ => $parent ); } return $retval ? 1 : 0; } sub units_for { my ($id) = @_; return undef if (! defined $terms->{$id}->{has_units}); return [ @{ $terms->{$id}->{has_units} } ]; } sub regex_for { my ($id) = @_; return undef if (! defined $terms->{$id}->{has_regexp}); croak "Multiple regular expressions not supported for $id\n" if (defined $terms->{$id}->{has_regexp}->[1]); my $rid = $terms->{$id}->{has_regexp}->[0]; return qr/$terms->{$rid}->{name}/; } sub print_tree { my ($cv, $level, @parents) = @_; croak "CV $cv not valid" if (! defined $roots{$cv}); $level = $level // 0; if (! @parents) { @parents = @{ $roots{$cv} }; } for my $parent (@parents) { next if (! defined $terms->{$parent}->{constant}); print "---" x $level . $parent, "\t" . $terms->{$parent}->{name}, "\t" . $terms->{$parent}->{constant}, "\n"; ++$level; if (defined $terms->{$parent}->{children}) { print_tree ($cv, $level, keys %{ $terms->{$parent}->{children}}); } --$level; } return; } 1; __END__ =head1 NAME MS::CV - interface to HUPO PSI controlled vocabularies =head1 SYNOPSIS use MS::CV qw/:MS :MOD :MI is_a regex_for units_for/; # use PSI terms directly as constants if ('MS:1000894' eq MS_RETENTION_TIME) { # do something } # check for child/parent relationships say "model param is valid!" if (is_a( MS_Q_TRAP, MS_INSTRUMENT_MODEL )); # PSI:MS conveniently provides cleavage regular expressions my $pep = 'PEPTIDERPEPTIDEKRAPPLE'; my $re = regex_for(MS_TRYPSIN); say $_ for split( $re, $pep ); =head1 DESCRIPTION C<MS::CV> provides a simple interface to the HUPO PSI controlled vocabularies. Currently the MS, MOD, and MI ontologies are indexed and available. The module utilizes a functional interface for speed and simplicity. It's primarily functionality is to export sets of constants (one for each ontology) directly mapping the term names to ids. =head1 CONSTANT NAMING Constant names are autogenerated from the C<name> field of the ontology OBO files. The rules for mapping are defined in the following code: my $symb = uc( $ontology . '_' . $term->{name} ); $symb =~ s/\W/_/g; $symb =~ s/^(\d)/_$1/; For example, the term "CRM spectrum" in the MS ontology becomes C<MS_CRM_SPECTRUM>. In addition, very rarely there are namespace collisions between terms after applying these transformations. In this case, increasing integer suffixes are appended to each colliding term. As of this writing, this only occurs for the following terms: =over 1 =item MOD_DESMOSINE MOD:00949 ("desmosine") becomes MOD_DESMOSINE_1 MOD:01933 ("desmosine") becomes MOD_DESMOSINE_2 =item MI_TEXT_MINING MI:0110 ("text mining") becomes MI_TEXT_MINING_1 MI:1056 ("text-mining") becomes MI_TEXT_MINING_2 =item MI_OPPOSING_EPISTASIS MI:1276 ("opposing epistasis") becomes MI_OPPOSING_EPISTASIS_1 MI:1285 ("opposing epistasis") becomes MI_OPPOSING_EPISTASIS_2 =back =head1 FUNCTIONS =head2 is_a if ( is_a( $child, $parent ) ) { say "model param is valid!"; } Takes two required arguments (child ID and parent ID) and returns a boolean value indicating whether the first term is a descendant of the second. =head2 units_for my $valid_units = units_for( $term ); Takes one argument (a CV ID) and returns a reference to an array of valid unit terms from the Unit Ontology, or undef if no units are defined. =head2 regex_for my $re = regex_for(MS_TRYPSIN); say $ for split( $re, $peptide ); Takes one argument (a CV ID representing a cleavage enzyme) and returns a regular expression that can be used to split a string based on the specificity of that enzyme. =head2 cv_name my $name = cv_name( $term ); Takes one argument (a CV ID) and returns the text description of the term =head2 print_tree print_tree ( 'MS' ); Takes one argument (a CV name) and prints a textual tree representation of the CV hierarchy to STDOUT (or the currently selected output filehandle). This is mainly of use for debugging the use of CV terms in your program, as it includes the constant name exported by this module for each term in the CV. =head1 CAVEATS AND BUGS Please report any bugs or feature requests to the issue tracker at L<https://github.com/jvolkening/p5-MS>. =head1 AUTHOR Jeremy Volkening <jdv@base2bio.com> =head1 COPYRIGHT AND LICENSE Copyright 2016-2017 Jeremy Volkening This program 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