Bio::Phenotype::OMIM::OMIMparser.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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).