Bio::Affymetrix
CDF
| Bio::Affymetrix::CDF- parse Affymetrix CDF files
 | 
| No package variables defined. | 
| use Bio::Affymetrix::CDF;
 # Parse the CDF file
 
 my $cdf=new CDF();
 
 $cdf->parse_from_file("foo.cdf");
 
 # Find some fun facts about this chip type
 
 print $cdf->rows().",".$cdf->cols()."\n";
 
 print $cdf->version()."\n";
 
 # Print out all of the probeset names on this chip type
 
 foreach my $i (@{$chp->probesets}) {
 print $i->name()."\n";
 }
 
 | 
| The Affymetrix microarray system produces files in a variety offormats. If this means nothing to you, these modules are probably not
 for you :). This module parses CDF files. Use this module if you want
 to find out about the design of an Affymetrix CHP, or you need the
 object for another one of the modules in this package.
 
 All of the Bio::Affymetrix modules parse a file entirely into
 memory. You therefore need enough memory to hold these objects. For
 some applications, parsing as a stream may be more appropriate-
 hopefully the source to these modules will give enough clues to make
 this an easy task. This module in particular takes a lot of memory if
 probe information is also stored (about 150Mb). Memory usage is not too
 onorous (about 15Mb) if probe level information is omitted.
 
 You fill the object filled with data using theparse_from_filehandle, parse_from_string or parse_from_file
 routines. You can get/set various statistics using methods on the
 object.
 
 The key method is probesets. This returns an array of
 Bio::Affymetrix::CDF::Probeset objects. These contain data about the
 probesets.
 
 | 
Methods description
  Arg [1]    : 	integer $cols (optional)
  Example    : 	my $name=$cdf->cols()
  Description: 	Get/set the number of cols in this chip
  Returntype : integer
  Exceptions : none
  Caller     : general
  Arg [1]    : 	string $name (optional)
  Example    : 	my $name=$cdf->name()
  Description: 	Get/set the name of this chip type (e.g. ATH1-121501)
  Returntype : string
  Exceptions : none
  Caller     : general
  Arg [0]    : none
  Example    : my $cdf=new Bio::Affymetrix::CDF();
  Description: constructor for CDF object
  Returntype : new Bio::Affmetrix::CDF object
  Exceptions : none
  Caller     : general
  Arg [0]    : 	none
  Example    : 	my $format=$cdf->original_format()
  Description:	Returns the format of the CDF file parsed. Currently
MAS5 only
  Returntype : 	string ("MAS5")
  Exceptions : 	none
  Caller     : 	general
  Arg [0]    : 	none
  Example    : 	my $max_units=$cdf->original_max_units()
  Description: 	Get the max unit number in the CDF file. Fairly useless.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Arg [0]    : 	none
  Example    : 	my $max_units=$cdf->original_num_qc_units()
  Description: 	Get the number of QC units in the CDF file. Only piece
of QC information obtainable using this piece of software.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Arg [0]    : 	none
  Example    : 	my $number_of_probes=$cdf->original_number_of_probes()
  Description: 	Get the number of probesets on the array, as listed
originally in the file. A better way is to do my
$q=scalar(@{$cdf->probesets()}); if you want a current count.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Arg [0]    : 	none
  Example    : 	my $version=$cdf->original_version()
  Description: 	Returns the version of the CDF file parsed. Encoded in file.
  Returntype : string
  Exceptions : none
  Caller     : general
  Arg [1]    : 	string
  Example    : 	$cdf->parse_from_file($cdf_filename);
  Description:	Parse a CDF file from a file
  Returntype :	none
  Exceptions : 	dies if can't open file
  Caller     : 	general
  Arg [1]    : 	reference to filehandle
  Example    : 	$cdf->parse_from_filehandle(\*STDIN);
  Description:	Parse a CDF file from a filehandle
  Returntype :	none
  Exceptions : 	none
  Caller     : 	general
  Arg [1]    : 	string
  Example    : 	$cdf->parse_from_string($cdf_file_in_a_string);
  Description:	Parse a CDF file from a buffer in memory
  Returntype :	none
  Exceptions : 	none
  Caller     : 	general
  Arg [1]    : 	arrayref $probesets 
  Example    : 	my @probesets=@{$cdf->probesets()}
  Description: 	Get the probesets on the array
  Returntype : an reference to an array of
Bio::Affymetrix::CDF::Probeset objects (q.v.)
  Exceptions : none
  Caller     : general
  Arg [1]    : 	integer $rows (optional)
  Example    : 	my $name=$cdf->rows()
  Description: 	Get/set the number of rows in this chip
  Returntype : integer
  Exceptions : none
  Caller     : general
Methods code
sub _next_line
 {    my $self=shift;
    my $q;
    
    my $fh=$self->{"FH"};
    do {
	$q=<$fh>;
	chomp $q;
    } while (!eof $fh&&$q=~/^\s*$/);
    if (!eof $fh) {
	return $q;
    } else {
	return undef;
    }}
sub _parse_chip_section
 {    my $self=shift;
    my $i;
    while (!(($i=$self->_next_line())=~/^\[.*\]$/)) {
	my ($name,$value)=$self->_split_line($i);
	$self->{uc $name}=$value;
    }
    return $i;}
sub _parse_qc_section
 {    my $self=shift;
    my $i;
    while (!(($i=$self->_next_line())=~/^\[.*\]$/)) {
	## This version doesn't do anything with QC sections. They bore us.
	;
    }
    return $i;}
sub _parse_unit_section
 {    my $self=shift;
    
    my $i=new Bio::Affymetrix::CDF::Probeset;
    my $ret=$i->_parse_from_filehandle($self->{"FH"});
    
    $i->CDF($self);
    
    push @{$self->{"PROBESETS"}},$i;
    
    return $ret;}
sub _split_line
 {    my $self=shift;
    my $line=shift;
    
    my @q=split /=/,$line,2;
    if (scalar(@q)!=2) {
	die "Can't parse line ".$line;
    }
    return @q;}
sub cols
 {    my $self=shift;
    if (my $q=shift) {
	$self->{"COLS"}=$q;
    }
    return $self->{"COLS"};}
sub name
 {    my $self=shift;
    if (my $q=shift) {
	$self->{"NAME"}=$q;
    }
    return $self->{"NAME"};}
sub new
 {    my $class=shift;
    my $q=shift;
    my $self={};
    $self->{"PROBESETS"}=[];
    bless $self,$class;
    return $self;}
sub original_format
 {    my $self=shift;
    return $self->{"FORMAT"};}
sub original_max_unit
 {    my $self=shift;
    return $self->{"MAXUNIT"};}
sub original_num_qc_units
 {    my $self=shift;
    return $self->{"NUMQCUNITS"};}
sub original_number_of_probes
 {    my $self=shift;
    return $self->{"NUMBEROFUNITS"};}
sub original_version
 {    my $self=shift;
    return $self->{"VERSION"};}
sub parse_from_file
 {    my $self=shift;
    my $filename=shift;
    open CDF,"<".$filename or die "Cannot open file ".$filename;
    $self->parse_from_filehandle(\*CDF);
    close CDF;}
sub parse_from_filehandle
 {    my $self=shift;
    $self->{"FH"}=shift;
    binmode $self->{"FH"},":crlf";
    ## Obtain file version, and do some rudimentary checking of information
    {
	my $i=$self->_next_line();
	if ($i ne "[CDF]") {
	    die "File does not look like a CDF file to me. Note- Bio::Affymetrix::CDF cannot understand all types CDF files";
	}
	$self->{"FORMAT"}="MAS5";
	$i=$self->_next_line();
	my ($name,$value)=$self->_split_line($i);
	if ($name ne "Version") {
	    die "File does not look like a CDF file to me";
	}
	if ($value ne "GC3.0") {
	    die "Can't understand any other type of CDF file other than GC3.0";
	}
	
	$self->{"VERSION"}=$value;
    }
    ## Parse the rest of the file
    my $i=$self->_next_line();
    while (!eof $self->{"FH"}) {
	if ($i eq "[Chip]") {
	    $i=$self->_parse_chip_section();
	} elsif ($i=~/\[QC\d+\]/) {
	    $i=$self->_parse_qc_section();
	} elsif ($i=~/\[Unit\d+\]/) {
	    $i=$self->_parse_unit_section();
	}
	
    }}
sub parse_from_string
 {    my $self=shift;
    my $string=shift;
    open CDF,"<",\$string or die "Cannot open string stream";
    $self->parse_from_filehandle(\*CDF);
    close CDF;}
sub probesets
 {    my $self=shift;
    if (my $q=shift) {
	$self->{"PROBESETS"}=$q;
    }
    return $self->{"PROBESETS"};}
sub rows
 {    my $self=shift;
    if (my $q=shift) {
	$self->{"ROWS"}=$q;
    }
    return $self->{"ROWS"};}
General documentation
| NOTES | top | 
|  | 
| REFERENCE | top | 
| Modules were written with the official Affymetrix documentation, whichcan be located at http://www.affymetrix.com/support/developer/AffxFileFormats.ZIP
 
 | 
| COMPATIBILITY | top | 
| This module can parse the CDF files produced by the Affymetrix softwareMAS 5 only. This is different from the Bio::Affymetrix::CHP
 module. These files have QC information in them, which is thrown away.
 
 | 
| TODO | top | 
| Writing CDF files as well as reading them. Parsing GCOS v1.2 CDFfiles. Maybe parse QC information?
 
 | 
| COPYRIGHT | top | 
| This module is free software. You can copy or redistribute it under the same terms as Perl itself.
 | 
| AUTHORS | top | 
|     Nick James (nick at arabidopsis.info)
 
 David J Craigon (david at arabidopsis.info)
 
 Nottingham Arabidopsis Stock Centre, University of Nottingham.
 
 |