Raw content of Bio::Phenotype::OMIM::OMIMparser # $Id: OMIMparser.pm,v 1.8.2.1 2003/03/25 12:32:16 heikki Exp $ # # BioPerl module for Bio::Phenotype::OMIM::OMIMparser # # Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com> # # (c) Christian M. Zmasek, czmasek@gnf.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME OMIMparser - parser for the OMIM database =head1 SYNOPSIS use Bio::Phenotype::OMIM::OMIMparser; # The OMIM database is available as textfile at: # ftp://ncbi.nlm.nih.gov/repository/OMIM/omim.txt.Z # The genemap is available as textfile at: # ftp://ncbi.nlm.nih.gov/repository/OMIM/genemap $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new( -genemap => "/path/to/genemap", -omimtext => "/path/to/omim.txt" ); while ( my $omim_entry = $omim_parser->next_phenotype() ) { # This prints everything. print( $omim_entry->to_string() ); print "\n\n"; # This gets individual data (some of them object-arrays) # (and illustrates the relevant methods of OMIMentry). my $numb = $omim_entry->MIM_number(); # *FIELD* NO my $title = $omim_entry->title(); # *FIELD* TI - first line my $alt = $omim_entry->alternative_titles_and_symbols(); # *FIELD* TI - additional lines my $mtt = $omim_entry->more_than_two_genes(); # "#" before title my $sep = $omim_entry->is_separate(); # "*" before title my $desc = $omim_entry->description(); # *FIELD* TX my $mm = $omim_entry->mapping_method(); # from genemap my $gs = $omim_entry->gene_status(); # from genemap my $cr = $omim_entry->created(); # *FIELD* CD my $cont = $omim_entry->contributors(); # *FIELD* CN my $ed = $omim_entry->edited(); # *FIELD* ED my $sa = $omim_entry->additional_references(); # *FIELD* SA my $cs = $omim_entry->clinical_symptoms(); # *FIELD* CS my $comm = $omim_entry->comment(); # from genemap my $mini_mim = $omim_entry->miniMIM(); # *FIELD* MN # A Bio::Phenotype::OMIM::MiniMIMentry object. # class Bio::Phenotype::OMIM::MiniMIMentry # provides the following: # - description() # - created() # - contributors() # - edited() # # Prints the contents of the MINI MIM entry (most OMIM entries do # not have MINI MIM entries, though). print $mini_mim->description()."\n"; print $mini_mim->created()."\n"; print $mini_mim->contributors()."\n"; print $mini_mim->edited()."\n"; my @corrs = $omim_entry->each_Correlate(); # from genemap # Array of Bio::Phenotype::Correlate objects. # class Bio::Phenotype::Correlate # provides the following: # - name() # - description() (not used) # - species() (always mouse) # - type() ("OMIM mouse correlate") # - comment() my @refs = $omim_entry->each_Reference(); # *FIELD* RF # Array of Bio::Annotation::Reference objects. my @avs = $omim_entry->each_AllelicVariant(); # *FIELD* AV # Array of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects. # class Bio::Phenotype::OMIM::OMIMentryAllelicVariant # provides the following: # - number (e.g ".0001" ) # - title (e.g "ALCOHOL INTOLERANCE" ) # - symbol (e.g "ALDH2*2" ) # - description (e.g "The ALDH2*2-encoded protein has a change ..." ) # - aa_ori (used if information in the form "LYS123ARG" is found) # - aa_mut (used if information in the form "LYS123ARG" is found) # - position (used if information in the form "LYS123ARG" is found) # - additional_mutations (used for e.g. "1-BP DEL, 911T") my @cps = $omim_entry->each_CytoPosition(); # from genemap # Array of Bio::Map::CytoPosition objects. my @gss = $omim_entry->each_gene_symbol(); # from genemap # Array of strings. # do something ... } =head1 DESCRIPTION This parser returns Bio::Phenotype::OMIM::OMIMentry objects (which inherit from Bio::Phenotype::PhenotypeI). It parses the OMIM database available as ftp://ncbi.nlm.nih.gov/repository/OMIM/omim.txt.Z together with (optionally) the gene map file at ftp://ncbi.nlm.nih.gov/repository/OMIM/genemap. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR Christian M. Zmasek Email: czmasek@gnf.org or cmzmasek@yahoo.com WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Phenotype::OMIM::OMIMparser; use vars qw( @ISA ); use strict; use Bio::Root::IO; use Bio::Root::Root; use Bio::Species; use Bio::Annotation::Reference; use Bio::Map::CytoPosition; use Bio::Phenotype::OMIM::OMIMentry; use Bio::Phenotype::OMIM::OMIMentryAllelicVariant; use Bio::Phenotype::Correlate; @ISA = qw( Bio::Root::Root ); use constant DEFAULT_STATE => 0; use constant MIM_NUMBER_STATE => 1; use constant TITLE_STATE => 2; use constant TEXT_STATE => 3; use constant MINI_MIM_TEXT_STATE => 4; use constant ALLELIC_VARIANT_STATE => 5; use constant SEE_ALSO_STATE => 6; use constant REF_STATE => 7; use constant SYMPT_STATE => 8; use constant CONTRIBUTORS_STATE => 9; use constant CREATED_BY_STATE => 10; use constant EDITED_BY_STATE => 11; use constant MINI_MIM_EDITED_BY_STATE => 12; use constant MINI_MIM_CREATED_BY_STATE => 13; use constant MINI_MIM_CONTRIBUTORS_STATE => 14; use constant TRUE => 1; use constant FALSE => 0; =head2 new Title : new Usage : $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new( -genemap => "/path/to/genemap", -omimtext => "/path/to/omim.txt" ); Function: Creates a new OMIMparser. Returns : A new OMIMparser object. Args : -genemap => the genemap file name (optional) -omimtext => the omim text file name =cut sub new { my( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my ( $genemap_file_name, $omimtxt_file_name ) = $self->_rearrange( [ qw( GENEMAP OMIMTEXT ) ], @args ); $self->init(); $genemap_file_name && $self->genemap_file_name( $genemap_file_name ); $omimtxt_file_name && $self->omimtxt_file_name( $omimtxt_file_name); return $self; } =head2 next_phenotype Title : next_phenotype() Usage : while ( my $omim_entry = $omim_parser->next_phenotype() ) { # do something with $omim_entry } Function: Returns an Bio::Phenotype::OMIM::OMIMentry or undef once the end of the omim text file is reached. Returns : A Bio::Phenotype::OMIM::OMIMentry. Args : =cut sub next_phenotype { my ( $self ) = @_; unless( defined( $self->_OMIM_text_file() ) ) { $self->_no_OMIM_text_file_provided_error(); } if ( $self->_done() == TRUE ) { return undef; } my $fieldtag = ""; my $contents = ""; my $line = ""; my $state = DEFAULT_STATE; my $saw_mini_min_flag = FALSE; my %record = (); while( $line = ( $self->_OMIM_text_file )->_readline() ) { if ( $line =~ /^\s*\*RECORD\*/ ) { if ( $self->_is_not_first_record() == TRUE ) { $self->_add_to_hash( $state, $contents,\%record ); my $omim_entry = $self->_createOMIMentry( \%record ); return $omim_entry; } else { $self->_is_not_first_record( TRUE ); } } elsif ( $line =~ /^\s*\*FIELD\*\s*(\S+)/ ) { $fieldtag = $1; if ( $state != DEFAULT_STATE ) { $self->_add_to_hash( $state, $contents,\%record ); } $contents = ""; if ( $fieldtag eq "NO" ) { $state = MIM_NUMBER_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "TI" ) { $state = TITLE_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "TX" ) { $state = TEXT_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "MN" ) { $state = MINI_MIM_TEXT_STATE; $saw_mini_min_flag = TRUE; } elsif ( $fieldtag eq "AV" ) { $state = ALLELIC_VARIANT_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "SA" ) { $state = SEE_ALSO_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "RF" ) { $state = REF_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "CS" ) { $state = SYMPT_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "CN" ) { if ( $saw_mini_min_flag == TRUE ) { $state = MINI_MIM_CONTRIBUTORS_STATE; } else { $state = CONTRIBUTORS_STATE; } } elsif ( $fieldtag eq "CD" ) { if ( $saw_mini_min_flag == TRUE ) { $state = MINI_MIM_CREATED_BY_STATE; } else { $state = CREATED_BY_STATE; } } elsif ( $fieldtag eq "ED" ) { if ( $saw_mini_min_flag == TRUE ) { $state = MINI_MIM_EDITED_BY_STATE; } else { $state = EDITED_BY_STATE; } } else { print "Warning: Unknown tag: $fieldtag\n"; } } else { $contents .= $line; } } $self->_OMIM_text_file()->close(); $self->_done( TRUE ); unless( %record ) { $self->_not_a_OMIM_text_file_error(); } $self->_add_to_hash( $state, $contents,\%record ); my $omim_entry = $self->_createOMIMentry( \%record ); return $omim_entry; } # next_phenotype =head2 init Title : init() Usage : $omim_parser->init(); Function: Initializes this OMIMparser to all "". Returns : Args : =cut sub init { my ( $self ) = @_; $self->genemap_file_name( "" ); $self->omimtxt_file_name( "" ); $self->_genemap_hash( {} ); $self->_OMIM_text_file( undef ); $self->_is_not_first_record( FALSE ); $self->_done( FALSE ); } # init =head2 genemap_file_name Title : genemap_file_name Usage : $omimparser->genemap_file_name( "genemap" ); Function: Set/get for the genemap file name. Returns : The genemap file name [string]. Args : The genemap file name [string] (optional). =cut sub genemap_file_name { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_genemap_file_name" } = $value; if ( $value =~ /\W/ ) { _genemap_hash( $self->_read_genemap( $value ) ); } } return $self->{ "_genemap_file_name" }; } # genemap_file_name =head2 omimtxt_file_name Title : omimtxt_file_name Usage : $omimparser->omimtxt_file_name( "omim.txt" ); Function: Set/get for the omim text file name. Returns : The the omim text file name [string]. Args : The the omim text file name [string] (optional). =cut sub omimtxt_file_name { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_omimtxt_file_name" } = $value; if ( $value =~ /\W/ ) { $self->_OMIM_text_file( new Bio::Root::IO->new( -file => $value ) ); } } return $self->{ "_omimtxt_file_name" }; } # omimtxt_file_name sub _createOMIMentry { my ( $self, $record_ref ) = @_; my $omim_entry = Bio::Phenotype::OMIM::OMIMentry->new(); my $mini_mim = Bio::Phenotype::OMIM::MiniMIMentry->new(); while ( ( my $key, my $val ) = each( %$record_ref ) ) { $val =~ s/^\s+//; $val =~ s/\s+$//; if ( $key == MIM_NUMBER_STATE ) { $val =~ s/\s+//g; $val =~ s/\D//g; $omim_entry->MIM_number( $val ); my $gm = $self->_genemap_hash(); if ( exists( $$gm{ $val } ) ) { $self->_parse_genemap( $omim_entry, $val ); } } elsif ( $key == TITLE_STATE ) { my ( $title, $alt_titles ) = $self->_parse_title( $val ); $omim_entry->title( $title ); $omim_entry->alternative_titles_and_symbols( $alt_titles ); if ( $title =~ /^\*/ ) { $omim_entry->is_separate( TRUE ); } elsif ( $title =~ /^#/ ) { $omim_entry->more_than_two_genes( TRUE ); } } elsif ( $key == TEXT_STATE ) { $omim_entry->description( $val ); } elsif ( $key == ALLELIC_VARIANT_STATE ) { my @allelic_variants = $self->_parse_allelic_variants( $val ); $omim_entry->add_AllelicVariants( @allelic_variants ); } elsif ( $key == SEE_ALSO_STATE ) { $omim_entry->additional_references( $val ); } elsif ( $key == REF_STATE ) { my @refs = $self->_parse_references( $val ); $omim_entry->add_References( @refs ); } elsif ( $key == SYMPT_STATE ) { $omim_entry->clinical_symptoms( $val ); } elsif ( $key == CONTRIBUTORS_STATE ) { $omim_entry->contributors( $val ); } elsif ( $key == CREATED_BY_STATE ) { $omim_entry->created( $val ); } elsif ( $key == EDITED_BY_STATE ) { $omim_entry->edited( $val ); } elsif ( $key == MINI_MIM_TEXT_STATE ) { $mini_mim->description( $val ); } elsif ( $key == MINI_MIM_CONTRIBUTORS_STATE ) { $mini_mim->contributors( $val ); } elsif ( $key == MINI_MIM_CREATED_BY_STATE ) { $mini_mim->created( $val ); } elsif ( $key == MINI_MIM_EDITED_BY_STATE ) { $mini_mim->edited( $val ); } } my $man = Bio::Species->new(); $man->classification( qw( sapiens Homo ) ); $man->common_name( "man" ); $omim_entry->species( $man ); $omim_entry->miniMIM( $mini_mim ); return $omim_entry; } # _createOMIMentry sub _parse_genemap { my ( $self, $omim_entry, $val ) = @_; my $genemap_line = ${ $self->_genemap_hash() }{ $val }; my @a = split( /\|/, $genemap_line ); my $locations = $a[ 4 ]; if ( defined ( $locations ) ) { $locations =~ s/\s+//g; my @ls = split( /[,;]/, $locations ); my @cps; foreach my $l ( @ls ) { my $cp = Bio::Map::CytoPosition->new( -value => $l ); push( @cps, $cp ); } $omim_entry->add_CytoPositions( @cps ); } my $gene_symbols = $a[ 5 ]; if ( defined ( $gene_symbols ) ) { $gene_symbols =~ s/\s+//g; my @gss = split( /[,;]/, $gene_symbols ); $omim_entry->add_gene_symbols( @gss ); } my $mouse_correlates = $a[ 16 ]; if ( defined ( $mouse_correlates ) ) { $mouse_correlates =~ s/\s+//g; my @mcs = split( /[,;]/, $mouse_correlates ); my @cs; foreach my $mc ( @mcs ) { my $mouse = Bio::Species->new(); $mouse->classification( qw( musculus Mus ) ); $mouse->common_name( "mouse" ); my $c = Bio::Phenotype::Correlate->new(); $c->name( $mc ); $c->species( $mouse ); $c->type( "OMIM mouse correlate" ); push( @cs, $c ); } $omim_entry->add_Correlates( @cs ); } $omim_entry->gene_status( $a[ 6 ] ) if defined $a[ 6 ]; $omim_entry->mapping_method( $a[ 10 ] ) if defined $a[ 10 ]; $omim_entry->comment( $a[ 11 ] ) if defined $a[ 11 ]; } # _parse_genemap sub _parse_allelic_variants { my ( $self, $text ) = @_; my @allelic_variants; my $number = ""; my $title = ""; my $symbol_mut_line = ""; my $prev_line = ""; my $description = ""; my $saw_empty_line = FALSE; my @lines = split( /\n/, $text ); foreach my $line ( @lines ) { if ( $line !~ /\w/ ) { $saw_empty_line = TRUE; } elsif ( $line =~ /^\s*(\.\d+)/ ) { my $current_number = $1; if ( $number ne "" ) { my $allelic_variant = $self->_create_allelic_variant( $number, $title, $symbol_mut_line, $description ); push( @allelic_variants, $allelic_variant ); } $number = $current_number; $title = ""; $prev_line = ""; $symbol_mut_line = ""; $description = ""; $saw_empty_line = FALSE; } elsif ( $title eq "" ) { $title = $line; } elsif ( $saw_empty_line == FALSE ) { $prev_line = $line; } elsif ( $saw_empty_line == TRUE ) { if ( $prev_line ne "" ) { $symbol_mut_line = $prev_line; $prev_line = ""; } if ( $description ne "" ) { $description .= "\n" . $line; } else { $description = $line; } } } my $allelic_variant = $self->_create_allelic_variant( $number, $title, $symbol_mut_line, $description ); push( @allelic_variants, $allelic_variant ); return @allelic_variants; } # _parse_allelic_variants sub _create_allelic_variant { my ( $self, $number, $title, $symbol_mut_line, $description ) = @_; my $symbol = ""; my $mutation = ""; my $aa_ori = ""; my $aa_mut = ""; my $position = ""; if ( $symbol_mut_line =~ /\s*(.+?)\s*,\s*([a-z]{3})(\d+)([a-z]{3})/i ) { $symbol = $1; $aa_ori = $2; $aa_mut = $4; $position = $3; } elsif ( $symbol_mut_line =~ /\s*(.+?)\s*,\s*(.+)/ ) { $symbol = $1; $mutation = $2; } else { $symbol = $symbol_mut_line; } if ( ! defined( $description ) ) { die( "undef desc" ); } if ( ! defined( $mutation ) ) { die( "undef mutation" ); } my $allelic_variant = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new(); $allelic_variant->number( $number ); $allelic_variant->aa_ori( $aa_ori ); $allelic_variant->aa_mut( $aa_mut ); $allelic_variant->position( $position ); $allelic_variant->title( $title ); $allelic_variant->symbol( $symbol ); $allelic_variant->description( $description ); $allelic_variant->additional_mutations( $mutation ); return $allelic_variant; } # _create_allelic_variant sub _parse_title { my ( $self, $text ) = @_; my $title = ""; if ( $text =~ /^(.+)\n/ ) { $title = $1; $text =~ s/^.+\n//; } else { $title = $text; $text = ""; } return ( $title, $text ); } # _parse_title sub _parse_references { my ( $self, $text ) = @_; $text =~ s/\A\s+//; $text =~ s/\s+\z//; $text =~ s/\A\d+\.\s*//; my @references; my @texts = split( /\s*\n\s*\n\s*\d+\.\s*/, $text ); foreach my $t ( @texts ) { my $authors = ""; my $title = ""; my $location = ""; $t =~ s/\s+/ /g; if ( $t =~ /(.+?)\s*:\s*(.+?[.?!])\s+(.+?)\s+(\S+?)\s*:\s*(\w?\d+.*)\s*,\s*(\d+)/ ) { $authors = $1; $title = $2; my $journal = $3; my $volume = $4; my $fromto = $5; my $year = $6; my $from = "", my $to = ""; if ( $fromto =~ /(\d+)-+(\d+)/ ) { $from = $1; $to = "-".$2; } elsif ( $fromto =~ /\A(\w+)/ ) { $from = $1; } $location = $journal." ".$volume." ".$from.$to." (".$year.")"; } elsif ( $t =~ /(.+?)\s*:\s*(.+?[.?!])\s*(.+?)\z/ ) { $authors = $1; $title = $2; $location = $3; } else { $title = $t; } my $ref = Bio::Annotation::Reference->new( -title => $title, -location => $location, -authors => $authors ); push( @references, $ref ); } return @references; } # _parse_references sub _genemap_hash { my ( $self, $value ) = @_; if ( defined $value ) { unless ( ref( $value ) eq "HASH" ) { $self->throw( "Argument to method \"_genemap_hash\" is not a reference to an Hash" ); } $self->{ "_genemap_hash" } = $value; } return $self->{ "_genemap_hash" }; } # _genemap_hash sub _is_not_first_record { my ( $self, $value ) = @_; if ( defined $value ) { unless ( $value == FALSE || $value == TRUE ) { $self->throw( "Found [$value] where [" . TRUE ." or " . FALSE . "] expected" ); } $self->{ "_not_first_record" } = $value; } return $self->{ "_not_first_record" }; } # _is_not_first_record sub _done { my ( $self, $value ) = @_; if ( defined $value ) { unless ( $value == FALSE || $value == TRUE ) { $self->throw( "Found [$value] where [" . TRUE ." or " . FALSE . "] expected" ); } $self->{ "_done" } = $value; } return $self->{ "_done" }; } # _done sub _OMIM_text_file { my ( $self, $value ) = @_; if ( defined $value ) { unless ( $value->isa( "Bio::Root::IO" ) ) { $self->throw( "[$value] is not a valid \"Bio::Root::IO\"" ); } $self->{ "_omimtxt_file" } = $value; } return $self->{ "_omimtxt_file" }; } # _OMIM_text_file sub _read_genemap { my ( $self, $genemap_file_name ) = @_; my $line = ""; my %genemap_hash = (); my $genemap_file = new Bio::Root::IO->new( -file => $genemap_file_name ); my @a = (); my %gm = (); while( $line = $genemap_file->_readline() ) { @a = split( /\|/, $line ); unless( scalar( @a ) == 18 ) { $self->throw( "Gene map file \"".$self->genemap_file_name() . "\" is not in the expected format" ); } $gm{ $a[ 9 ] } = $line; } $genemap_file->close(); $self->_genemap_hash( \%gm ); } #_read_genemap sub _no_OMIM_text_file_provided_error { my ( $self ) = @_; my $msg = "Need to indicate a OMIM text file to read from with\n"; $msg .= "either \"OMIMparser->new( -omimtext => \"path/to/omim.txt\" );\"\n"; $msg .= "or \"\$omim_parser->omimtxt_file_name( \"path/to/omim.txt\" );\""; $self->throw( $msg ); } # _no_OMIM_text_file_provided_error sub _not_a_OMIM_text_file_error { my ( $self ) = @_; my $msg = "File \"".$self->omimtxt_file_name() . "\" appears not to be a OMIM text file"; $self->throw( $msg ); } # _not_a_OMIM_text_file_error sub _add_to_hash { my ( $self, $state, $contents, $record_ref ) = @_; if ( exists( $record_ref->{ $state } ) ) { chomp( $record_ref->{ $state } ); $record_ref->{ $state } = $record_ref->{ $state } . $contents; } else { $record_ref->{ $state } = $contents; } } # _add_to_hash 1;