Bio::Tools Prints
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Summary
Bio::Tools::Prints - Parser for FingerPRINTScanII program
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Generic
Inherit
Bio::Root::IO Bio::Root::Root
Synopsis
  use Bio::Tools::Prints;
my $prints_parser = Bio::Tools::Prints->new(-fh =>$filehandle );
while( my $prints_feat = $prints_parser->next_result ) {
push @prints_feat, $prints_feat;
}
Description
 PRINTScan II is a PRINTS fingerprint identification algorithm.
Copyright (C) 1998,1999 Phil Scordis
Methods
newDescriptionCode
next_resultDescriptionCode
create_featureDescriptionCode
print_sacDescriptionCode
seqnameDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tools::Prints->new(-fh=>$filehandle);
Function: Builds a new Bio::Tools::Prints object
Returns : Bio::Tools::Prints
Args : -filename
-fh (filehandle)
next_resultcodeprevnextTop
 Title   : next_result
Usage : my $feat = $prints_parser->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args : none
create_featurecodeprevnextTop
 Title   : create_feature
Usage : my $feat=$prints_parser->create_feature($feature,$seqname)
Function: creates a SeqFeature Generic object
Returns : Bio::SeqFeature::FeaturePair
Args :
print_saccodeprevnextTop
 Title   : print_sac
Usage : $prints_parser->print_sac($print_sac)
Function: get/set for print_sac
Returns :
Args :
seqname codeprevnextTop
 Title   : seqname
Usage : $prints_parser->seqname($seqname)
Function: get/set for seqname
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
      my($class,@args) = @_;

      my $self = $class->SUPER::new(@args);
      $self->_initialize_io(@args);

      return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($self) = @_;
    my %printsac;
    my @features;
    my $line;
    my $sequenceId;
     
    while ($_=$self->_readline()) {
      
           $line = $_;
           chomp $line;

           if ($line =~ s/^Sn;//) { # We have identified a Sn; line so there should be the following:
($sequenceId) = $line =~ /^\s*(\w+)/; $self->seqname($sequenceId); next; } if ($line =~ s/^1TBH//) { my ($id) = $line =~ /^\s*(\w+)/; my ($ac) = $line =~ /(PR\w+)\s*$/; $printsac{$id} = $ac; $self->print_sac(\%printsac); next; } if ($line =~ s/^3TB//) { if ($line =~ s/^[HN]//) { my($num)=""; $line =~ s/^\s+//; my @elements = split /\s+/, $line; my ($fingerprintName,$motifNumber,$temp,$tot,$percentageIdentity,$profileScore,$pvalue,$subsequence,$motifLength,$lowestMotifPosition,$matchPosition,$highestMotifPosition) = @elements; my $start = $matchPosition; my $end = $matchPosition + $motifLength - 1; my $print_sac = $self->print_sac; my %printsac = %{$print_sac}; my $print = $printsac{$fingerprintName}; my $seqname=$self->seqname; my $feat = "$print,$start,$end,$percentageIdentity,$profileScore,$pvalue"; my $new_feat = $self->create_feature($feat,$seqname); return $new_feat; } if ($line =~ s/^F//) { return; } next; } next; }
}
create_featuredescriptionprevnextTop
sub create_feature {
    my ($self, $feat,$sequenceId) = @_;

    my @f = split (/,/,$feat);
    # create feature object
my $feature= Bio::SeqFeature::Generic->new( -seq_id =>$sequenceId, -start=>$f[1], -end => $f[2], -score => $f[4], -source => "PRINTS", -primary =>$f[0], -logic_name => "PRINTS", ); $feature->add_tag_value('evalue',$f[5]); $feature->add_tag_value('percent_id',$f[3]); my $feature2 = Bio::SeqFeature::Generic->new( -seq_id => $f[0], -start => 0, -end => 0, ); my $fp = Bio::SeqFeature::FeaturePair->new( -feature1 => $feature, -feature2 => $feature2 ); return $fp;
}
print_sacdescriptionprevnextTop
sub print_sac {
    my $self = shift;
    return $self->{'print_sac'} = shift if @_;
    return $self->{'print_sac'};
}
seqnamedescriptionprevnextTop
sub seqname {
    my($self,$seqname)=@_;
    return $self->{'seqname'}=$seqname if(defined($seqname));
    return $self->{'seqname'};
}

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 - Balamurugan KumarasamyTop
 bala@tll.org.sg
juguang@tll.org.sg
APPENDIXTop
 The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _