NAME
Bio::Phenotype::OMIM::OMIMparser - parser for the OMIM database
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_raw(); # *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 ...
}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.
FEEDBACK
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://bioperl.org/wiki/Mailing_lists - About the mailing listsSupport
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
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 the web:
https://github.com/bioperl/bioperl-live/issuesAUTHOR
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 namenext_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 :init
Title : init()
Usage : $omim_parser->init();
Function: Initializes this OMIMparser to all "".
Returns :
Args :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).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).