FFTable of Contents

Module to access FIGfamsfamily_dirfamily_functionfamily_idlist_membersnewpegs_ofrepresentativesshould_be_memberModule to access FIGfamsnewusage my $figfam_obj = FF->new($fam_id, $fam_dir);

$fam_id is the ID of the family, of the form FIGnnnnnn where n is a digit it is required.

$fam_data is require as the directory that contains (or will contain) FigFam data.

pegs_ofusage print $figfam_obj->pegs_of();

Returns a list of just pegs.

list_membersusage @ids = $figfam_obj->list_members();

Returns a list of the PEG FIDs in a family.

representativesusage @rep_seqs = $figfam_obj->representatives();

Returns a list of the "representative sequences" characterizing a FIGfam.

should_be_memberusage if ( $figfam_obj->should_be_member( $seq ) ) { #...do something... }

Returns ($placed,$sims). $placed will be TRUE if the protein sequence in $seq is judged to b "similar enough" to the members of a family to potentially be included.

I have added the "loose" argument as an optional last argument. This means that

if ( $figfam_obj->should_be_member( $seq,0,1 ) ) { #...do something... }

will return true, even if the input sequence is truncated (i.e., we do not force th similarity to go across 80% of matched sequences in the family).

family_functionusage $func = $figfam_obj->family_function();

Returns the "consensus function" assigned to a FIGfam object.

family_idusage $fam_id = $figfam_obj->family_id();

Returns the FIGfam ID of a FIGfam object.

family_dirusage:

C<< $dir = &FigFam::family_dir( $fam_data, $fam_id ); >>Returns the path to the subdirectory of $fam_data$fam_id