Bio::Matrix::PSM::IO transfac
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Summary
Bio::Matrix::PSM::IO::transfac - PSM transfac parser
Package variables
No package variables defined.
Included modules
Bio::Annotation::Comment
Bio::Annotation::DBLink
Bio::Annotation::Reference
Bio::Matrix::PSM::Psm
Bio::Root::Root
strict
Inherit
Bio::Matrix::PSM::IO Bio::Matrix::PSM::PsmHeader
Synopsis
See Bio::Matrix::PSM::IO for documentation
Description
#
Methods
newDescriptionCode
next_psmDescriptionCode
_parse_matrix
No description
Code
_make_matrixDescriptionCode
_parse_ref
No description
Code
DESTROY
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'transfac',
-file=>$file);
Function: Associates a file with the appropriate parser
Throws :
Example :
Args :
Returns : "Bio::Matrix::PSM::$format"->new(@args);
next_psmcodeprevnextTop
 Title   : next_psm
Usage : my $psm=$psmIO->next_psm();
Function: Reads the next PSM from the input file, associated with this object
Throws : Upon finding a line, defining the matrix, where one or more positions
are not defined, see _make_matrix
Returns : Bio::Matrix::PSM::Psm object
Args : none
_make_matrixcodeprevnextTop
 Title   : _make_matrix
Usage :
Function:
Throws : If a position is undefined, for example if you have line like this
in the file you are parsing: 08 4,7,,9
Example : Internal stuff
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
    my ($class,@args)=@_;
    my $line;
    my $self = $class->SUPER::new(@args);
    my ($file)=$self->_rearrange(['FILE'], @args);
    $self->_initialize_io(@args) || warn "Did you intend to use STDIN?"; #Read only for now
#Remove header
do { $line=$self->_readline; chomp $line; push @{$self->{unstructured}},$line if (length($line)>2); } until ($line =~ m{^//}) || (!defined($line)); #Unstructured header
$self->_initialize; return $self;
}
next_psmdescriptionprevnextTop
sub next_psm {
    my $self=shift;
    my $line;
    return if ($self->{end});
    my (@a,@c,@g,@t, $id, $tr1, @refs,$accn, $bf, $sites);
    my $i=0;
    while (defined( $line=$self->_readline)) {
	chomp($line);
	if ($line=~/^\d{2}/) {	#Begining of the frequency data
($a[$i],$c[$i],$g[$i],$t[$i])=_parse_matrix($line); $i++; } ($tr1,$accn)=split(/\s{2}/,$line) if ($line=~/^AC\s/); ($tr1,$bf)=split(/\s{2}/,$line) if ($line=~/^BF\s/); ($tr1,$id)=split(/\s{2}/,$line) if ($line=~/^ID\s/); last if (($line=~/^XX/) && ($i>0)); } if (!(defined($id) && defined($accn))) { $self->{end}=1; return; } while (defined( $line=$self->_readline)) { #How many sites?
if ($line=~/^BA\s/) { my ($tr1,$ba)=split(/\s{2}/,$line); ($sites)=split(/\s/,$ba); } if ($line=~/^RN/) { #Adding a reference as Bio::Annotation object (self)
# not interested in RN line itself, since has only transfac-specific
# reference id? - no push back of line
my $ref=_parse_ref($self); push @refs,$ref } last if ($line=~m{^//}); } # We have the frequencies, let's create a SiteMatrix object
my %matrix = &_make_matrix($self,\@a,\@c,\@g,\@t,$id, $accn); $matrix{-sites}=$sites if ($sites); $matrix{-width}=@a; my $psm=Bio::Matrix::PSM::Psm->new(%matrix); foreach my $ref (@refs) { $psm->add_Annotation('reference',$ref); } return $psm;
}
_parse_matrixdescriptionprevnextTop
sub _parse_matrix {
    my $line=shift;
    $line=~s/\s+/,/g;
my ($tr,$a,$c,$g,$t)=split(/,/,$line); return $a,$c,$g,$t;
}
_make_matrixdescriptionprevnextTop
sub _make_matrix {
    my ($a, $c, $g, $t, @fa, @fc,@fg, @ft, @a,@c,@g,@t);
    my $ave=0;
    my ($self,$cA,$cC,$cG,$cT, $id, $accn)= @_;

    for (my $i=0; $i < @{$cA};$i++) {
	#No value can be undefined -throw an exception, since setting to 0 probably would be wrong
#If this happens it would indicate most probably that the file, being parsed is in a different format
map { $self->throw('Parsing error, a position is not defined') unless defined(${$_}[$i]) } ($cA, $cG, $cC, $cT); if ( (${$cA}[$i] + ${$cC}[$i] + ${$cG}[$i] + ${$cT}[$i] ) ==0 ) { push @a,$ave; push @c,$ave; push @g,$ave; push @t,$ave; } else { push @a,${$cA}[$i]; push @c,${$cC}[$i]; push @g,${$cG}[$i]; push @t,${$cT}[$i]; $ave = ((${$cA}[$i]+${$cC}[$i]+ ${$cG}[$i]+${$cT}[$i]) / 4 +$ave)/2; } } for (my $i=0; $i<@a;$i++) { my $zero=($a[$i]+$c[$i]+$g[$i]+$t[$i]); next if ($zero==0); push @fa, $a[$i]; push @fc, $c[$i]; push @fg, $g[$i]; push @ft, $t[$i]; } return (-pA=>\@fa,-pC=>\@fc,-pG=>\@fg,-pT=>\@ft, -id=>$id, -accession_number=>$accn)
}
_parse_refdescriptionprevnextTop
sub _parse_ref {
my $self=shift;
my ($authors,$title,$loc,@refs,$tr,$db,$dbid);
    while (my $refline=$self->_readline) { #Poorely designed, should go through an array with fields
chomp $refline; my ($field,$arg)=split(/\s+/,$refline,2); last if ($field=~/XX/); $field.=' '; REF: { if ($field=~/RX/) { #DB Reference
$refline=~s/[;\.]//g;
($tr, $db, $dbid)=split(/\s+/,$refline); last REF; } if ($field=~/RT/) { #Title
$title .= $arg; last REF; } if ($field=~/RA/) { #Author
$authors .= $arg; last REF; } if ($field=~/RL/) { #Journal
$loc .= $arg; last REF; } } } my $reference=Bio::Annotation::Reference->new(-authors=>$authors, -title=>$title, -location=>$loc); if ($db eq 'MEDLINE') { # does it ever equal medline?
$reference->medline($dbid); } elsif ($dbid) { $reference->pubmed($dbid); } return $reference;
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self=shift;
    $self->close;
}

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 one
of the Bioperl mailing lists. 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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Stefan KirovTop
Email skirov@utk.edu
APPENDIXTop
_parseMatrixTop
 Title   : _parseMatrix
Usage :
Function: Parses a line
Throws :
Example : Internal stuff
Returns : array (frequencies for A,C,G,T in this order).
Args : string