[Bioperl-l] sample code for Bio::Phenotype::OMIM::OMIMparser

[Hilmar Lapp]

Can you include verbatim the error messages you're getting? -hilmar

> -----Original Message-----
> From: Leonardo Kenji Shikida [mailto:kenji@vettatech.com]
> Sent: Wednesday, December 11, 2002 12:49 PM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] sample code for Bio::Phenotype::OMIM::OMIMparser
> 
> 
> I am trying to use this class, so I just cut and paste it the 
> example. I 
> would like to transform into a tabular representation to put 
> inside my 
> local DB. It works great for all the $main[x] below, but 
> doesn't for the 
> $mini_mim array. Probably I am referencing something wrong here.
> 
> any help is welcome.
> 
> > 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  => "genemap.txt",
> >                                                         
> -omimtext => "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).
> >     $main[0]  = $omim_entry->MIM_number();                  
>    # *FIELD* NO
> >     $main[1] = $omim_entry->title();                        
>   # *FIELD* TI - first line
> >     $main[2]   = 
> $omim_entry->alternative_titles_and_symbols(); # *FIELD* TI - 
> additional lines
> >     $main[3]   = $omim_entry->more_than_two_genes();        
>     # "#" before title
> >     $main[4]   = $omim_entry->is_separate();                
>     # "*" before title
> >     $main[5]  = $omim_entry->description();                 
>    # *FIELD* TX
> >     $main[6]    = $omim_entry->mapping_method();            
>      # from genemap
> >     $main[7]    = $omim_entry->gene_status();               
>      # from genemap
> >     $main[8]    = $omim_entry->created();                   
>      # *FIELD* CD
> >     $main[9]  = $omim_entry->contributors();                
>    # *FIELD* CN
> >     $main[10]    = $omim_entry->edited();                   
>       # *FIELD* ED
> >     $main[11]    = $omim_entry->additional_references();    
>       # *FIELD* SA
> >     $main[12]    = $omim_entry->clinical_symptoms();        
>       # *FIELD* CS
> >     $main[13]  = $omim_entry->comment();                    
>     # from genemap
> > 
> >     $numb = $main[0];
> > 
> >     foreach $x (@main){
> > 
> > 	$x =~ s/\t//g;
> >     	$x =~ s/\n//g;
> >     	$x =~ s/'/`/g;
> > 
> >     }
> > 
> 
> 
> WORKS HERE
> 
> 
> 
> >     print MAIN join("\t",@main);
> > 
> > 
> >     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()
> 
> 
> BUT NOT HERE. neither $x nor $mini_min
> 
> > 
> >     foreach my $x ($mini_mim){
> > 
> > 	    print MIM 
> "$numb\t$x->description()\t$mini_mim->created()\t$mini_min->co
> ntributors()\t$mini_mim->edited()\n";
> > 
> >     }
> 
> thanks in advance
> 
> Kenji
> 
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