|
/export/home/cpanrun/depot/main/contrib-patched/perl/CPAN/src/Bio-Affymetrix/blib/lib/Bio/Affymetrix/CDF/Probeset.pm |
Bio::Affymetrix::CDF::Probeset- an Affymetrix probeset in an CDF file
use Bio::Affymetrix::CDF;
# Parse the CDF file
my $cdf=new Bio::Affymetrix::CDF();
$cdf->parse_from_file(``foo.cdf'');
# Print out the probeset name of Unit 1001
my $probeset=$cdf->probesets()->{1001};
print $probeset->name();
The Affymetrix microarray system produces files in a variety of formats. If this means nothing to you, these modules are probably not for you :). After these modules have parsed a CDF file, the resulting Bio::Affymetrix::CDF file contains a hash of Bio::Affmetrix::CDF::Probeset objects, keyed on the unit number. This allows you look at the details of the probeset.
If you have parsed a CDF file with probe-level parsing turned on, you can examine the individual probes using the probes method. By altering the contents of this array, you can redesign the chip! NASC use this in our cross-species work (http://affymetrix.arabidopsis.info/xspecies).
You can only get probe-level information if you have parsed the CDF object with probe-level parsing turned on.
The probe level parsing interface is a bit inelegant at the moment. This might change in future versions.
Copyright (C) 2005 by Nick James, David J Craigon, NASC (arabidopsis.info), The University of Nottingham
This module is free software. You can copy or redistribute it under the same terms as Perl itself.
Affymetrix is a registered trademark of Affymetrix Inc., Santa Clara, California, USA.
Nick James (nick at arabidopsis.info)
David J Craigon (david at arabidopsis.info)
Nottingham Arabidopsis Stock Centre (http://arabidopsis.info), University of Nottingham.
Arg [0] : none Example : my $cdf=new Bio::Affymetrix::CDF::Probeset(); Description: constructor for Bio::Affymetrix::CDF::Probeset object. You probably do not want to make these objects yourself yet, however. Returntype : new Bio::Affmetrix::CDF::Probeset object Exceptions : none Caller : general
unit_name()
Description: Always NONE for expression arrays. Only available in MAS5 files
Returntype : string
Exceptions : none
Caller : general
=cutsub unit_name { my $self=shift;
if (my $q=shift) {
$self->{"UNITNAME"}=$q;
}
return $self->{"UNITNAME"};
}
# Sense or anti sense probeset? Returns true, or false
is_sense()) { .... }
Description: Returns true when this is a sense (rather than
anti-sense) probeset. Only available in MAS5 files
Returntype : boolean
Exceptions : none
Caller : general
=cutsub is_sense { my $self=shift;
if (my $q=shift) {
$self->{"SENSE"}=$q;
}
return $self->{"SENSE"};
}
# These are all named ``original_'' because they aren't calculated, they are what a parsed file claims
# number of probepairs making up the probeset
original_num_probepairs()
Description: Get the number of probepairs in this probeset
Returntype : integer
Exceptions : none
Caller : general
=cutsub original_num_probepairs { my $self=shift; return $self->{``NUMATOMS''}; }
# number of squares making up the probeset
=head2 original_num_probes
Arg [0] : none
Example : my $probepairs=$ps->original_num_probes()
Description: Get the number of probes in this probeset
Returntype : integer
Exceptions : none
Caller : general
=cut
sub original_num_probes { my $self=shift; return $self->{``NUMCELLS''}; }
# arbitrary number for the probeset
unit_number()
Description: Get the unit number of this probeset (a unique number
assigned to each probe in the CDF file but otherwise meaningless)
Returntype : integer
Exceptions : none
Caller : general
=cutsub original_unit_number { my $self=shift; return $self->{``UNITNUMBER''}; }
sub unit_number { my $self=shift; carp ``unit_number is deprecated. Use original_unit_number instead (same function only renamed)''; $self->original_unit_number(@_); }
# type of unit as an ENUM like thing
unit_type()
Description: Get/Set the unit number of this probeset. Probably expression only
Returntype : one of ``CustomSeq'', ``genotyping'', ``expression'', ``tag/GenFlex''
Exceptions : none
Caller : general
=cutsub unit_type { my $self=shift;
if (my $q=shift) {
if ($q eq "CustomSeq") {
$self->{"UNITTYPE"}=1;
} elsif ($q eq "genotyping") {
$self->{"UNITTYPE"}=2;
} elsif ($q eq "expression") {
$self->{"UNITTYPE"}=3;
} elsif ($q eq "tag/GenFlex") {
$self->{"UNITTYPE"}=7;
} else {
die "Not a valid unit type";
}
}
if ($self->{"UNITTYPE"}==1) {
return "CustomSeq";
} elsif ($self->{"UNITTYPE"}==2) {
return "genotyping";
} elsif ($self->{"UNITTYPE"}==3) {
return "expression";
} elsif ($self->{"UNITTYPE"}==7) {
return "tag/GenFlex";
}
}
## Censor this?
sub original_number_blocks { my $self=shift; return $self->{``NUMBERBLOCKS''}; }
# 0= substitution 1= insertion 2=deletion. No effort made here- we # don't really do genotyping arrays
sub mutation_type { my $self=shift;
if (my $q=shift) {
$self->{"MUTATIONTYPE"}=$q;
}
return $self->{"MUTATIONTYPE"};
}
name()
Description: Get/set name of probeset
Returntype : string
Exceptions : none
Caller : general
=cutsub name { my $self=shift;
if (my $q=shift) {
$self->{"NAME"}=$q;
}
return $self->{"NAME"};
}
probe_pairs()
Description: Get/set list of probe pairs making up this array. Only available if
with probes mode is used.
Returns an reference to an array of "probe pairs". Each "probe pair"
is an array reference containing two Bio::Affymetrix::CDF::Probe
objects.
The design of the CDF file implies that one point chips with 3
mismatch probes and one perfect match probe were mooted, but we
are unsure whether any of these were ever released to the
public. Nevertheless, these modules are ready!
Returntype : reference to array of arrayrefs of Bio::Affymetrix::CDF::Probe objects Exceptions : none Caller : general =cut
sub probe_pairs { my $self=shift; if (!$self->{``probemode''}) { die ``Probes is not available when not in probemode''; }
if (my $q=shift) {
$self->{"PROBES"}=$q;
}
return $self->{"PROBES"};
}
sub probes { my $self=shift;
carp ("probes deprecated. Use probe_pairs instead");
$self->probe_pairs(@_);
}
probes()
Description: Get/set CDF object this probeset belongs to.
Returntype : Bio::Affymetrix::CDF object
Exceptions : none
Caller : general
=cutsub CDF { my $self=shift;
if (my $q=shift) {
$self->{"CDF"}=$q;
}
return $self->{"CDF"};
}
# Parses from FileHandle
sub _parse_from_filehandle { my $self=shift; my $fh=shift;
$self->{"probemode"}=shift;
$self->{"FH"}=$fh;
# Handle trivia from unit header
my $i;
while (defined($i=<$fh>) && (!($i=~/^\[.*\]$/o))) {
if ($i=~/^([^=]+)=(.*)$/o) {
my $name=$1;
my $value=$2;
if (uc $name eq "NAME") {
$self->{"UNITNAME"}=$value;
} elsif (uc $name eq "DIRECTION") {
$self->{"SENSE"}=($value==1);
} else {
$self->{uc $name}=$value;
}
}
}
# Block section
while (defined($i=<$fh>) && (!($i=~/^\[.*\]$/o))) {
if ($i=~/^([^=]+)=(.*)$/o) {
my $name=$1;
my $value=$2;
if ($self->{"probemode"}&&$name=~/Cell\d+/o) {
my $h= new Bio::Affymetrix::CDF::Probe();
my @s=split /\t/,$value;
$h->{"NAME"}=$name;
$h->{"X"}=$s[0];
$h->{"Y"}=$s[1];
$h->{"PROBE"}=$s[2];
$h->{"EXPOS"}=$s[5];
$h->{"POS"}=$s[6];
$h->{"PBASE"}=$s[8];
$h->{"TBASE"}=$s[9];
$h->{"ATOM"}=$s[10];
$h->{"INDEX"}=$s[11];
$h->{"PROBESET"}=$self;
push @{$self->{"PROBES"}->[$h->{"ATOM"}]},$h;
$self->{"CDF"}->{"PROBEGRID"}->[$h->{"X"}][$h->{"Y"}]=$h;
} elsif (uc $name eq "NAME") {
$self->{"NAME"}=$value;
}
}
}
return $i;
}
# Parses from FileHandle for XDA format file
sub _parse_from_filehandle_bin { my $self=shift; my $fh=shift;
$self->{"probemode"}=shift;
$self->{"FH"}=$fh;
# Handle trivia from unit header
my $buffer;
# General header information
(read ($fh, $buffer, 20)==20) or die "Can no longer read from file";
($self->{"UNITTYPE"},$self->{"DIRECTION"},$self->{"NUMATOMS"},undef,$self->{"NUMCELLS"},$self->{"UNITNUMBER"},$self->{"ATOMSPERCELL"})=unpack ("SCV4C",$buffer);
# Translate UNITTYPE into equivalent numbers for MAS5
if ($self->{"UNITTYPE"}==1) {
$self->{"UNITTYPE"}=3;
} elsif ($self->{"UNITTYPE"}==2) {
$self->{"UNITTYPE"}=2;
} elsif ($self->{"UNITTYPE"}==3) {
$self->{"UNITTYPE"}=1;
} elsif ($self->{"UNITTYPE"}==4) {
$self->{"UNITTYPE"}=7;
}
# Block information- we assume one block only since we only do expression arrays
$self->{"NUMBERBLOCKS"}=1;
(read ($fh, $buffer, 82)==82) or die "Can no longer read from file";
{
my @temp=unpack ("V2C2V2Z64",$buffer);
$self->{"NAME"}=$temp[6];
}
$self->{"UNITNAME"}="NONE";
$self->{"PROBES"}=[];
for (my $i=1;$i<=$self->{"NUMCELLS"};$i++) {
(read ($fh, $buffer, 14)==14) or die "Can no longer read from file";
if ($self->{"probemode"}) {
my $h= new Bio::Affymetrix::CDF::Probe();
($h->{"ATOM"},$h->{"X"},$h->{"Y"},$h->{"POS"},$h->{"PBASE"},$h->{"TBASE"})=unpack("VS2VC2",$buffer);
$h->{"INDEX"}=$i;
$h->{"PBASE"}=uc(chr($h->{"PBASE"}));
$h->{"TBASE"}=uc(chr($h->{"TBASE"}));
$h->{"PROBESET"}=$self;
push @{$self->{"PROBES"}->[$h->{"ATOM"}]},$h;
$self->{"CDF"}->{"PROBEGRID"}->[$h->{"X"}][$h->{"Y"}]=$h;
}
}
}
1;
|
/export/home/cpanrun/depot/main/contrib-patched/perl/CPAN/src/Bio-Affymetrix/blib/lib/Bio/Affymetrix/CDF/Probeset.pm |