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revision 1.503, Tue Jul 25 22:07:01 2006 UTC revision 1.504, Sun Jul 30 01:43:56 2006 UTC
# Line 10702  Line 10702 
10702    
10703  =head3 families_for_protein  =head3 families_for_protein
10704    
10705  use: @families = $fig->families_for_protein($peg)  C<< my @families = $fig->families_for_protein($peg); >>
10706    
10707  This takes any type of protein identifier (e.g. fig, swissprot, kegg, etc) and returns an array of families that this protein is in.  Return a list of all the families containing the specified protein.
10708    
10709  Notes:  =over 4
10710  1. This is really a wrapper to prot_to_cid and then in_family, but this is what you will likely use most of the time  
10711    =item peg
10712    
10713    ID of the PEG representing the protein in question.
10714    
10715    =item RETURN
10716    
10717    Returns a list of the IDs of the families containing the protein.
10718    
10719    =back
10720    
10721  =cut  =cut
10722    
# Line 10721  Line 10730 
10730    
10731  =head3 proteins_in_family  =head3 proteins_in_family
10732    
10733  use @proteins = $fig->proteins_in_family($family);  C<< my @proteins = $fig->proteins_in_family($family); >>
10734    
10735  This takes a family id as an argument and returns every protein id known to be in that family.  Return a list of every protein in a family.
10736    
10737  Note: this is also really a wrapper around a couple of other methods, but they will always be called together so this makes it a little cleaner.  =over 4
10738    
10739    =item family
10740    
10741    ID of the relevant protein family.
10742    
10743    =item RETURN
10744    
10745    Returns a list of all the proteins in the specified family.
10746    
10747    =back
10748    
10749  =cut  =cut
10750    
# Line 10743  Line 10762 
10762    
10763  =head3 family_function  =head3 family_function
10764    
10765  usage: $func = $fig->family_function($family)  C<< my $func = $fig->family_function($family); >>
10766    
10767  Returns the putative function of all of the pegs in $family.  Remember, we  Returns the putative function of all of the pegs in a protein family.  Remember, we
10768  are defining "protein family" as a set of homologous proteins that have the  are defining "protein family" as a set of homologous proteins that have the
10769  same function.  same function.
10770    
10771    =over 4
10772    
10773    =item family
10774    
10775    ID of the relevant protein family.
10776    
10777    =item RETURN
10778    
10779    Returns the name of the function assigned to the members of the specified family.
10780    
10781    =back
10782    
10783  =cut  =cut
10784    
10785  sub family_function {  sub family_function {
# Line 10769  Line 10800 
10800    
10801  =head3 sz_family  =head3 sz_family
10802    
10803  usage: $n = $fig->sz_family($family)  C<< my $n = $fig->sz_family($family); >>
10804    
10805    Returns the number of proteins in a family.
10806    
10807  Returns the number of cids in $family.  =over 4
10808    
10809    =item family
10810    
10811    ID of the relevant protein family.
10812    
10813    =item RETURN
10814    
10815    Returns the number of proteins in the specified family.
10816    
10817    =back
10818    
10819  =cut  =cut
10820    

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