Bio::Factory FTLocationFactory
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Summary
Bio::Factory::FTLocationFactory - A FeatureTable Location Parser
Package variables
No package variables defined.
Included modules
Bio::Location::Fuzzy
Bio::Location::Simple
Bio::Location::Split
Inherit
Bio::Factory::LocationFactoryI Bio::Root::Root
Synopsis
    # parse a string into a location object
$loc = Bio::Factory::FTLocationFactory->from_string("join(100..200,
400..500");
Description
Implementation of string-encoded location parsing for the Genbank feature
table encoding of locations.
Methods
BEGIN Code
from_stringDescriptionCode
_parse_locationDescriptionCode
Methods description
from_stringcode    nextTop
 Title   : from_string
Usage : $loc = $locfactory->from_string("100..200");
Function: Parses the given string and returns a Bio::LocationI implementing
object representing the location encoded by the string.
This implementation parses the Genbank feature table encoding of locations. Example : Returns : A Bio::LocationI implementing object. Args : A string.
_parse_locationcodeprevnextTop
 Title   : _parse_location
Usage : $loc = $locfactory->_parse_location( $loc_string)
Function: Parses the given location string and returns a location object with start() and end() and strand() set appropriately. Note that this method is private. Returns : A Bio::LocationI implementing object or undef on failure Args : location string
Methods code
BEGINTop
BEGIN {
    # the below is an optimized regex obj. from J. Freidl's Mastering Reg Exp.
$LOCREG = qr{
(?>
[^()]+
|
\(
(??{
$LOCREG})
\)
)*
}
from_stringdescriptionprevnextTop
sub from_string {
    my ($self,$locstr,$op) = @_;
    my $loc;
    
    #$self->debug("$locstr\n");
# $op for operator (error handling)
# run on first pass only
# Note : These location types are now deprecated in GenBank (Oct. 2006)
if (!defined($op)) { # convert all (X.Y) to [X.Y]
$locstr =~ s{\((\d+\.\d+)\)}{\[$1\]}g; # convert ABC123:(X..Y) to ABC123:[X..Y]
# we should never see the above
$locstr =~ s{:\((\d+\.{2}\d+)\)}{:\[$1\]}g; } if ($locstr =~ m{(.*?)\(($LOCREG)\)(.*)}o) { # any matching parentheses?
my ($beg, $mid, $end) = ($1, $2, $3); my (@sublocs) = (split(q(,),$beg), $mid, split(q(,),$end)); my @loc_objs; my $loc_obj; SUBLOCS: while (@sublocs) { my $subloc = shift @sublocs; next if !$subloc; my $oparg = ($subloc eq 'join' || $subloc eq 'bond' || $subloc eq 'order' || $subloc eq 'complement') ? $subloc : undef; # has operator, requires further work (recurse)
if ($oparg) { my $sub = shift @sublocs; # simple split operators (no recursive calls needed)
if (($oparg eq 'join' || $oparg eq 'order' || $oparg eq 'bond' ) && $sub !~ m{(?:join|order|bond)}) { my @splitlocs = split(q(,), $sub); $loc_obj = Bio::Location::Split->new(-verbose => 1, -splittype => $oparg); while (my $splitloc = shift @splitlocs) { next unless $splitloc; my $sobj; if ($splitloc =~ m{\(($LOCREG)\)}) { my $comploc = $1; $sobj = $self->_parse_location($comploc); $sobj->strand(-1); } else { $sobj = $self->_parse_location($splitloc); } $loc_obj->add_sub_Location($sobj); } } else { $loc_obj = $self->from_string($sub, $oparg); # reinsure the operator is set correctly for this level
# unless it is complement
$loc_obj->splittype($oparg) unless $oparg eq 'complement'; } } # no operator, simple or fuzzy
else { $loc_obj = $self->from_string($subloc,1); } $loc_obj->strand(-1) if ($op && $op eq 'complement'); push @loc_objs, $loc_obj; } my $ct = @loc_objs; if ($op && !($op eq 'join' || $op eq 'order' || $op eq 'bond') && $ct > 1 ) { $self->throw("Bad operator $op: had multiple locations ". scalar(@loc_objs).", should be SplitLocationI"); } if ($ct > 1) { $loc = Bio::Location::Split->new(); $loc->add_sub_Location(shift @loc_objs) while (@loc_objs); return $loc; } else { $loc = shift @loc_objs; return $loc; } } else { # simple location(s)
$loc = $self->_parse_location($locstr); $loc->strand(-1) if ($op && $op eq 'complement'); } return $loc;
}
_parse_locationdescriptionprevnextTop
sub _parse_location {
    my ($self, $locstr) = @_;
    my ($loc, $seqid);
    #$self->debug( "Location parse, processing $locstr\n");
# 'remote' location?
if($locstr =~ m{^(\S+):(.*)$}o) { # yes; memorize remote ID and strip from location string
$seqid = $1; $locstr = $2; } # split into start and end
my ($start, $end) = split(/\.\./, $locstr); # remove enclosing parentheses if any; note that because of parentheses
# possibly surrounding the entire location the parentheses around start
# and/or may be asymmetrical
# Note: these are from X.Y fuzzy locations, which are deprecated!
$start =~ s/(?:^\[+|\]+$)//g if $start; $end =~ s/(?:^\[+|\]+$)//g if $end; # Is this a simple (exact) or a fuzzy location? Simples have exact start
# and end, or is between two adjacent bases. Everything else is fuzzy.
my $loctype = ".."; # exact with start and end as default
$loctype = '?' if ( ($locstr =~ /\?/) && ($locstr !~ /\?\d+/) ); my $locclass = "Bio::Location::Simple"; if(! defined($end)) { if($locstr =~ /(\d+)([\.\^])(\d+)/) { $start = $1; $end = $3; $loctype = $2; $locclass = "Bio::Location::Fuzzy" unless (abs($end-$start) <= 1) && ($loctype eq "^"); } else { $end = $start; } } # start_num and end_num are for the numeric only versions of
# start and end so they can be compared
# in a few lines
my ($start_num, $end_num) = ($start,$end); if ( ($start =~ /[\>\<\?\.\^]/) || ($end =~ /[\>\<\?\.\^]/) ) { $locclass = 'Bio::Location::Fuzzy'; if($start =~ /(\d+)/) { ($start_num) = $1; } else { $start_num = 0 } if ($end =~ /(\d+)/) { ($end_num) = $1; } else { $end_num = 0 } } my $strand = 1; if( $start_num > $end_num && $loctype ne '?') { ($start,$end,$strand) = ($end,$start,-1); } # instantiate location and initialize
$loc = $locclass->new(-verbose => $self->verbose, -start => $start, -end => $end, -strand => $strand, -location_type => $loctype); # set remote ID if remote location
if($seqid) { $loc->is_remote(1); $loc->seq_id($seqid); } # done (hopefully)
return $loc; } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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 BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
CONTRIBUTORSTop
Jason Stajich, jason-at-bioperl-dot-org
Chris Fields, cjfields-at-uiuc-dot-edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 Title   : new
Usage : my $obj = Bio::Factory::FTLocationFactory->new();
Function: Builds a new Bio::Factory::FTLocationFactory object
Returns : an instance of Bio::Factory::FTLocationFactory
Args :