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Bio-Affymetrix
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lib/Bio/Affymetrix/CHP.pm  view on Meta::CPAN 

=cut


sub original_number_qc_units {
    my $self=shift;
    return $self->{"no_qc_units"};
}

# MS COM prog ID

=head2 original_com_progid

  Arg [0]    : 	none
  Example    : 	my $com_id=$chp->original_com_progid()
  Description:	Gets the progid of the original Microsoft COM object that made
				this CHP file
  Returntype :	string
  Exceptions : 	none
  Caller     : 	general

=cut

sub original_com_progid {
    my $self=shift;
    return $self->{"com_progid"};
}

# CEL file name this CHP file originated from

=head2 CEL_file_name

  Arg [1]    : 	string $cel_file_name (optional)
  Example    : 	my $cel_file_name=$chp->CEL_file_name();
  Description:	Get/set the CEL file this CHP file was made from
  Returntype :	string

lib/Bio/Affymetrix/CHP.pm  view on Meta::CPAN 

    ($self->{"no_cols"},$self->{"no_rows"},$self->{"no_units"},$self->{"no_qc_units"})= unpack ("S2V2", $buffer);

    read ($fh, $buffer, 4);
    
    $self->{"chip_type"}=unpack ("V", $buffer);

    if ($self->{"chip_type"}!=0) {
	croak "This software does not process non-expression arrays";
    }
    
    $self->{"com_progid"}=$self->unpack_length_string($fh);
    
    $self->{"cel_file_name"}=$self->unpack_length_string($fh);

    $self->{"probe_array_type"}=$self->unpack_length_string($fh);

    $self->{"algorithm_name"}=$self->unpack_length_string($fh);

    $self->{"algorithm_version"}=$self->unpack_length_string($fh);

    # Algorithm parameters

lib/Bio/Affymetrix/CHP.pm  view on Meta::CPAN 

    # THROW AWAY PROBESET NUMBER FOR EACH PROBESET
    read ($fh, $buffer, 4*$self->{"no_units"});

    read ($fh, $buffer, 512);
    ($self->{"probe_array_type"},$self->{"cel_file_name"})=unpack ("Z256Z256",$buffer);

    if ($self->{"probe_array_type"} ne $self->{"cdf"}->name()) {
	carp "The CDF object you have supplied does not have the same name as the CDF file used to make this CHP file. Results may be dubious";
    }

    $self->{"com_progid"}=$self->unpack_length_string($fh);

    # Actual data. This is the bit that would need to be added to, if we did SNP etc. arrays
    {
	my %data;
	
	if ($self->{"version"}==12) {
	    
	    my %results;
	    
	    my $probesetlist=$self->{"cdf"}->probesets();

pdoc/Affymetrix/CHP.html  view on Meta::CPAN 

<TR><TD><B>_parse_mas5</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE3">Code</A></TD></TR>
<TR><TD><B>_parse_xda</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE4">Code</A></TD></TR>
<TR><TD><B>_write_mas5</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE5">Code</A></TD></TR>
<TR><TD><B>_write_xda</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE6">Code</A></TD></TR>
<TR><TD><B>algorithm_name</B></TD><TD><A HREF="#POD3">Description</A></TD><TD><A HREF="#CODE7">Code</A></TD></TR>
<TR><TD><B>algorithm_params</B></TD><TD><A HREF="#POD4">Description</A></TD><TD><A HREF="#CODE8">Code</A></TD></TR>
<TR><TD><B>algorithm_version</B></TD><TD><A HREF="#POD5">Description</A></TD><TD><A HREF="#CODE9">Code</A></TD></TR>
<TR><TD><B>background_zones</B></TD><TD><A HREF="#POD6">Description</A></TD><TD><A HREF="#CODE10">Code</A></TD></TR>
<TR><TD><B>cols</B></TD><TD><A HREF="#POD7">Description</A></TD><TD><A HREF="#CODE11">Code</A></TD></TR>
<TR><TD><B>new</B></TD><TD><A HREF="#POD8">Description</A></TD><TD><A HREF="#CODE12">Code</A></TD></TR>
<TR><TD><B>original_com_progid</B></TD><TD><A HREF="#POD9">Description</A></TD><TD><A HREF="#CODE13">Code</A></TD></TR>
<TR><TD><B>original_file_name</B></TD><TD><A HREF="#POD10">Description</A></TD><TD><A HREF="#CODE14">Code</A></TD></TR>
<TR><TD><B>original_format</B></TD><TD><A HREF="#POD11">Description</A></TD><TD><A HREF="#CODE15">Code</A></TD></TR>
<TR><TD><B>original_number_of_probes</B></TD><TD><A HREF="#POD12">Description</A></TD><TD><A HREF="#CODE16">Code</A></TD></TR>
<TR><TD><B>original_number_qc_units</B></TD><TD><A HREF="#POD13">Description</A></TD><TD><A HREF="#CODE17">Code</A></TD></TR>
<TR><TD><B>original_version</B></TD><TD><A HREF="#POD14">Description</A></TD><TD><A HREF="#CODE18">Code</A></TD></TR>
<TR><TD><B>parse_from_file</B></TD><TD><A HREF="#POD15">Description</A></TD><TD><A HREF="#CODE19">Code</A></TD></TR>
<TR><TD><B>parse_from_filehandle</B></TD><TD><A HREF="#POD16">Description</A></TD><TD><A HREF="#CODE20">Code</A></TD></TR>
<TR><TD><B>parse_from_string</B></TD><TD><A HREF="#POD17">Description</A></TD><TD><A HREF="#CODE21">Code</A></TD></TR>
<TR><TD><B>probe_array_type</B></TD><TD><A HREF="#POD18">Description</A></TD><TD><A HREF="#CODE22">Code</A></TD></TR>
<TR><TD><B>probe_set_results</B></TD><TD><A HREF="#POD19">Description</A></TD><TD><A HREF="#CODE23">Code</A></TD></TR>

pdoc/Affymetrix/CHP.html  view on Meta::CPAN 

<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_background_zones"></A><A NAME="POD6"></A><B>background_zones</B></TD><TD><A HREF="#CODE10">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD5">prev</A></TD><TD><A HREF="#POD7">next</A></...
<pre>  Arg [1]    : 	arrayref of arrayrefs $background_zones (optional)<BR>  Example    : 	my @background_zones=@{$chp-&gt;background_zones()};<BR><BR># Print &quot;X&quot;, &quot;Y&quot;, &quot;Background Value&quot; for background zone 0<BR>print $...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_cols"></A><A NAME="POD7"></A><B>cols</B></TD><TD><A HREF="#CODE11">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD6">prev</A></TD><TD><A HREF="#POD8">next</A></TD></TR></TABLE>
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $x=$chp-&gt;cols()<BR>  Description:	Numbers of columns in the array <BR>  Returntype :	integer<BR>  Exceptions : 	none<BR>  Caller     : 	general<BR></pre>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_new"></A><A NAME="POD8"></A><B>new</B></TD><TD><A HREF="#CODE12">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD7">prev</A></TD><TD><A HREF="#POD9">next</A></TD></TR></TABLE>
<pre>  Arg [1]    : Bio::Affymetrix::CDF $db_file<BR>  Example    : my $chp=new <B>Bio::Affymetrix::CHP</B>($cdf);<BR>  Description: constructor for CHP object<BR>  Returntype : new Bio::Affmetrix::CHP object<BR>  Exceptions : none<BR>  Caller     : ...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_com_progid"></A><A NAME="POD9"></A><B>original_com_progid</B></TD><TD><A HREF="#CODE13">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD8">prev</A></TD><TD><A HREF="#POD10">nex...
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $com_id=$chp-&gt;original_com_progid()<BR>  Description:	Gets the progid of the original Microsoft COM object that made<BR>				this CHP file<BR>  Returntype :	string<BR>  Exceptions : 	none<BR>  Caller ...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_file_name"></A><A NAME="POD10"></A><B>original_file_name</B></TD><TD><A HREF="#CODE14">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD9">prev</A></TD><TD><A HREF="#POD11">next...
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $chp_file_name=$chp-&gt;original_file_name();<BR>  Description:	If this object was created using parse_from_file, the original filename. Otherwise undef.<BR>  Returntype :	string<BR>  Exceptions : 	none...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_format"></A><A NAME="POD11"></A><B>original_format</B></TD><TD><A HREF="#CODE15">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD10">prev</A></TD><TD><A HREF="#POD12">next</A><...
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $format=$chp-&gt;original_format()<BR>  Description: 	Returns the format of the CHP file parsed<BR>  			 	(currently) either &quot;XDA&quot; (which is a GCOS v1.2 format,<BR>				also known as version 4)...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_number_of_probes"></A><A NAME="POD12"></A><B>original_number_of_probes</B></TD><TD><A HREF="#CODE16">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD11">prev</A></TD><TD><A HRE...
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $original_probes=$chp-&gt;original_number_of_probes()<BR>  Description:	Gets the original number of probes reported in the<BR>				array.<BR><BR>				The CHP files have the number of probes stored in<BR>	...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">

pdoc/Affymetrix/CHP.html  view on Meta::CPAN 

    <font color="#ff0000">## THROW AWAY PROBESETTYPE FOR EACH PROBESET</font><BR>    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4*<font color="...
    <font color="#ff0000">## THROW AWAY PROBESET NUMBER FOR EACH PROBESET</font><BR>    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4*<font colo...

    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 512<font color="#0000ff"><b>)</b></font>;
    <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"probe_array_type"</font><font color="#0000ff"><b>}</b></font>,<font color="#1f32ff">$self</font>-&gt;<font col...

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"probe_array_type"</font><font color="#0000ff"><b>}</b></font> <font col...
	carp <font color="#007400">"The CDF object you have supplied does not have the same name as the CDF file used to make this CHP file. Results may be dubious"</font>;
    <font color="#0000ff"><b>}</b></font>

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"com_progid"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font><fo...

    <font color="#ff0000">## Actual data. This is the bit that would need to be added to, if we did SNP etc. arrays</font><BR>    <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%data</font>;
	
	<font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"version"</font><font color="#0000ff"><b>}</b></font>==12<font color="#0000...
	    
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">%results</font>;
	    
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$probesetlist</font>=<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"cdf"</font><font color="#0000ff"><b>}</b></font>-&gt;<font color...

pdoc/Affymetrix/CHP.html  view on Meta::CPAN 

    <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"no_cols"</font><font color="#0000ff"><b>}</b></font>,<font color="#1f32ff">$self</font>-&gt;<font color="#0000...

    <font color="#4169e1"><b>read</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$fh</font>, <font color="#1f32ff">$buffer</font>, 4<font color="#0000ff"><b>)</b></font>;
    
    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"chip_type"</font><font color="#0000ff"><b>}</b></font>=<font color="#4169e1"><b>unpack</b></font> <font color="#0000ff"><b>(</b></font><font color=...

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"chip_type"</font><font color="#0000ff"><b>}</b></font>!=0<font color="#...
	croak <font color="#007400">"This software does not process non-expression arrays"</font>;
    <font color="#0000ff"><b>}</b></font>
    
    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"com_progid"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font><fo...
    
    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"cel_file_name"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font>...

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"probe_array_type"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</fo...

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_name"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</font...

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"algorithm_version"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$self</font>-&gt;<font color="#ff8204">unpack_length_string</f...

    <font color="#ff0000">## Algorithm parameters</font><BR>

pdoc/Affymetrix/CHP.html  view on Meta::CPAN 

    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>  = <font color="#0000ff"><b>{</b></font><font color="#0000ff"><b>}</b></font>;

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"cdf"</font><font color="#0000ff"><b>}</b></font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>(</b></font>!<font color="#4169e1"><b>defined</b></font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="...
	croak <font color="#007400">"Need to supply a Bio::Affymetric::CDF file to Bio::Affymetrix::CHP constructor"</font>;
    <font color="#0000ff"><b>}</b></font>

    <font color="#4169e1"><b>bless</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>, <font color="#1f32ff">$class</font><font color="#0000ff"><b>)</b></font>;          <font color="#ff0000">## reconsecrate</font><BR>...
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE13"></A><B>original_com_progid</B></TD><TD><A HREF="#POD9">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE12">prev</A></TD><TD WIDTH="30"><A HREF="#CODE14"...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_com_progid</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"com_progid"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE14"></A><B>original_file_name</B></TD><TD><A HREF="#POD10">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE13">prev</A></TD><TD WIDTH="30"><A HREF="#CODE15"...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_file_name</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"file_name"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE15"></A><B>original_format</B></TD><TD><A HREF="#POD11">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE14">prev</A></TD><TD WIDTH="30"><A HREF="#CODE16">ne...
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_format</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;



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