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 lists
Support¶
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/issues
AUTHOR¶
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 92121
APPENDIX¶
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 name
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 :
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).