NAME
Bio::SeqIO::scf - .scf file input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class, see Bio::SeqIO for more information.
DESCRIPTION
This object can transform .scf files to and from Bio::Seq::SeqWithQuality objects. Mechanisms are present to retrieve trace data from scf files.
FEEDBACK
Mailing Lists
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://www.bioperl.org/MailList.shtml - About the mailing listsReporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/AUTHOR Chad Matsalla
Chad Matsalla bioinformatics@dieselwurks.com
CONTRIBUTORS
Jason Stajich, jason@bioperl.org Tony Cox, avc@sanger.ac.uk Heikki Lehvaslaiho, heikki@ebi.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_seq()
Title : next_seq()
Usage : $scf = $stream->next_seq()
Function: returns the next scf sequence in the stream
Returns : Bio::Seq::SeqWithQuality object
Args : NONE
Notes : Fills the interface specification for SeqIO.
The SCF specification does not provide for having more then
one sequence in a given scf. So once the filehandle has been open
and passed to SeqIO don't expect to run this function more then
once on a given scf unless you embraced and extended the SCF
standard. (But that's just C R A Z Y talk, isn't it.)_set_v3_quality()
Title : _set_v3_quality()
Usage : $self->_set_v3_quality()
Function: Set the base qualities from version3 scf's
Returns : Nothing. Alters $self.
Args : None.
Notes : _set_v3_peak_indices($buffer)
Title : _set_v3_peak_indices($buffer)
Usage : $self->_set_v3_peak_indices($buffer);
Function: Unpacks the base accuracies for version3 scf
Returns : Nothing. Alters $self
Args : A scalar containing binary data.
Notes : _set_v3_base_accuracies($buffer)
Title : _set_v3_base_accuracies($buffer)
Usage : $self->_set_v3_base_accuracies($buffer)
Function: Set the base accuracies for version 3 scf's
Returns : Nothing. Alters $self.
Args : A scalar containing binary data.
Notes : _set_comments($buffer)
Title : _set_comments($buffer)
Usage : $self->_set_comments($buffer);
Function: Gather the comments section from the scf and parse it into its
components.
Returns : Nothing. Modifies $self.
Args : The buffer. It is expected that the buffer contains a binary
string for the comments section of an scf file according to
the scf file specifications.
Notes : None. Works like Jello._set_header()
Title : _set_header($buffer)
Usage : $self->_set_header($buffer);
Function: Gather the header section from the scf and parse it into its
components.
Returns : Nothing. Modifies $self.
Args : The buffer. It is expected that the buffer contains a binary
string for the header section of an scf file according to the
scf file specifications.
Notes : None._set_v2_bases($buffer)
Title : _set_v2_bases($buffer)
Usage : $self->_set_v2_bases($buffer);
Function: Gather the bases section from the scf and parse it into its
components.
Returns : Nothing. Modifies $self.
Args : The buffer. It is expected that the buffer contains a binary
string for the bases section of an scf file according to the
scf file specifications.
Notes : None._set_v2_traces(\@traces_array)
Title : _set_v2_traces(\@traces_array)
Usage : $self->_set_v2_traces(\@traces_array);
Function: Parses an scf Version2 trace array into its base components.
Returns : Nothing. Modifies $self.
Args : A reference to an array of the unpacked traces section of an
scf version2 file.get_trace($base_channel)
Title : get_trace($base_channel)
Usage : @a_trace = @{$obj->get_trace("A")};
Function: Return the trace data for the given base.
Returns : A reference to an array containing the trace data for the
given base.
Args : A,C,G, or T. Any other input throws.
Notes :get_peak_indices()
Title : get_peak_indices()
Usage : @a_trace = @{$obj->get_peak_indices()};
Function: Return the peak indices for this scf.
Returns : A reference to an array containing the peak indices for this scf.
Args : None.
Notes :get_header()
Title : get_header()
Usage : %header = %{$obj->get_header()};
Function: Return the header for this scf.
Returns : A reference to a hash containing the header for this scf.
Args : None.
Notes :_dump_traces_incoming($transformed)
Title : _dump_traces_incoming("transformed")
Usage : &_dump_traces($ra,$rc,$rg,$rt);
Function: Used in debugging. Prints all traces one beside each other.
Returns : Nothing.
Args : References to the arrays containing the traces for A,C,G,T.
Notes : Beats using dumpValue, I'll tell ya. Much better then using
join' ' too.
- if a scalar is included as an argument (any scalar), this
procedure will dump the _delta'd trace. If you don't know what
that means you should not be using this._dump_traces_outgoing($transformed)
Title : _dump_traces_outgoing("transformed")
Usage : &_dump_traces_outgoing(($ra,$rc,$rg,$rt);
Function: Used in debugging. Prints all traces one beside each other.
Returns : Nothing.
Args : References to the arrays containing the traces for A,C,G,T.
Notes : Beats using dumpValue, I\'ll tell ya. Much better then using
join' ' too.
- if a scalar is included as an argument (any scalar), this
procedur will dump the _delta'd trace. If you don't know what
that means you should not be using this.write_seq
Title : write_seq(-SeqWithQuality => $swq, <comments>)
Usage : $obj->write_seq( -SeqWithQuality => $swq,
-version => 2,
-CONV => "Bioperl-Chads Mighty SCF writer.");
Function: Write out an scf.
Returns : Nothing.
Args : Requires: a reference to a SeqWithQuality object to form the
basis for the scf.
if -version is provided, it should be "2" or "3". A SCF of that
version will be written.
Any other arguments are assumed to be comments and are put into
the comments section of the scf. Read the specifications for scf
to decide what might be good to put in here.
Notes :
Someday: (All of this stuff is easy easy easy I just don't have
the requirement or the time.)
- Change the peak scaling factor?
- Change the width of the peak?
- Change the overlap between peaks?_set_binary_header()
Title : _set_binary_header();
Usage : $self->_set_binary_header();
Function: Provide the binary string that will be used as the header for
a scfv2 document.
Returns : A binary string.
Args : None. Uses the entries in the $self->{'header'} hash. These
are set on construction of the object (hopefully correctly!).
Notes : _set_binary_tracesbases($version,$sequence,$ref_quality)
Title : _set_binary_tracesbases($version,$sequence,$ref_quality)
Usage : $self->_set_binary_tracesbases($version,$sequence,
$ref_quality);
Function: Constructs the trace and base strings for all scfs
Returns : Nothing. Alters self.
Args : $version - "2" or "3"
$sequence - a scalar containing arbitrary sequence data
$ref_quality - a reference to an array containing quality
values
Notes : This is a really complicated thing._make_trace_string($version)
Title : _make_trace_string($version)
Usage : $self->_make_trace_string($version)
Function: Merges trace data for the four bases to produce an scf
trace string. _requires_ $version
Returns : Nothing. Alters $self.
Args : $version - a version number. "2" or "3"
Notes : _set_binary_comments(\@comments)
Title : _set_binary_comments(\@comments)
Usage : $self->_set_binary_comments(\@comments);
Function: Provide a binary string that will be the comments section of
the scf file. See the scf specifications for detailed
specifications for the comments section of an scf file. Hint:
CODE=something\nBODE=something\n\0
Returns : Nothing. Alters self.
Args : A reference to an array containing comments.
Notes : None._fill_missing_data($swq)
Title : _fill_missing_data($swq)
Usage : $self->_fill_missing_data($swq);
Function: If the $swq with quality has no qualities, set all qualities
to 0.
If the $swq has no sequence, set the sequence to N's.
Returns : Nothing. Modifies the SeqWithQuality that was passed as an
argument.
Args : A reference to a Bio::Seq::SeqWithQuality
Notes : None._delta(\@trace_data,$direction)
Title : _delta(\@trace_data,$direction)
Usage : $self->_delta(\@trace_data,$direction);
Function:
Returns : A reference to an array containing modified trace values.
Args : A reference to an array containing trace data and a string
indicating the direction of conversion. ("forward" or
"backward").
Notes : This code is taken from the specification for SCF3.2.
http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_unix_4.html_unpack_magik($buffer)
Title : _unpack_magik($buffer)
Usage : $self->_unpack_magik($buffer)
Function: What unpack specification should be used? Try them all.
Returns : Nothing.
Args : A buffer containing arbitrary binary data.
Notes : Eliminate the ambiguity and the guesswork. Used in the
adaptation of _delta(), mostly.read_from_buffer($filehandle,$buffer,$length)
Title : read_from_buffer($filehandle,$buffer,$length)
Usage : $self->read_from_buffer($filehandle,$buffer,$length);
Function: Read from the buffer.
Returns : $buffer, containing a read of $length
Args : a filehandle, a buffer, and a read length
Notes : I just got tired of typing
"unless (length($buffer) == $length)" so I put it here._dump_keys()
Title : _dump_keys()
Usage : &_dump_keys($a_reference_to_some_hash)
Function: Dump out the keys in a hash.
Returns : Nothing.
Args : A reference to a hash.
Notes : A debugging method._dump_base_accuracies()
Title : _dump_base_accuracies()
Usage : $self->_dump_base_accuracies();
Function: Dump out the v3 base accuracies in an easy to read format.
Returns : Nothing.
Args : None.
Notes : A debugging method._dump_peak_indices_incoming()
Title : _dump_peak_indices_incoming()
Usage : $self->_dump_peak_indices_incoming();
Function: Dump out the v3 peak indices in an easy to read format.
Returns : Nothing.
Args : None.
Notes : A debugging method._dump_base_accuracies_incoming()
Title : _dump_base_accuracies_incoming()
Usage : $self->_dump_base_accuracies_incoming();
Function: Dump out the v3 base accuracies in an easy to read format.
Returns : Nothing.
Args : None.
Notes : A debugging method._dump_comments()
Title : _dump_comments()
Usage : $self->_dump_comments();
Function: Debug dump the comments section from the scf.
Returns : Nothing.
Args : Nothing.
Notes : None.