Fwd: [Bioperl-l] example on how to use Bio::Phenotype::OMIM::OMIMparser

[Hilmar Lapp]

Chris, can you change $parser->next() to the more redundant naming 
convention we chose for bioperl parsers being 
$parser->next_<interface_name_without_the_trailing_I>(). I.e., this 
would be next_phenotype() here.

	-hilmar

Begin forwarded message:

> From: "Chris Zmasek" <czmasek@gnf.org>
> Date: Mon Sep 16, 2002  07:03:42 PM US/Pacific
> To: <bioperl-l@bioperl.org>
> Subject: [Bioperl-l] example on how to use 
> Bio::Phenotype::OMIM::OMIMparser
>
>
> Hi!
>
>
> This is an example on how to use Bio::Phenotype::OMIM::OMIMparser 
> and the associated classes (OMIMentry, MiniMIMentry, Correlate, 
> OMIMentryAllelicVariant):
>
>
>
>   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() ) {
>
>     # 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
>       # Array of Bio::Phenotype::OMIM::MiniMIMentry objects.
>       # class Bio::Phenotype::OMIM::MiniMIMentry
>       # provides the following:
>       # - description()
>       # - created()
>       # - contributors()
>       # - edited()
>
>
>     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.
>
>    }
>
> Christian Zmasek [czmasek@gnf.org]
>
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> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------