Bio::SeqIO::scf(3)

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::SequenceTrace 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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Support
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 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 the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR Chad Matsalla
Chad Matsalla bioinformatics@dieselwurks.com

CONTRIBUTORS
Jason Stajich, jason@bioperl.org Tony Cox, avc@sanger.ac.uk Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Nancy Hansen, nhansen at mail.nih.gov

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 : a Bio::Seq::SequenceTrace 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 do not expect to run this function more then
           once on a given scf unless you embraced and extended the SCF
       standard.  SCF comments are accessible through the Bio::SeqI
           interface method annotation().

  _get_v3_quality()
 Title   : _get_v3_quality()
 Usage   : $self->_get_v3_quality()
 Function: Set the base qualities from version3 scf
 Returns : Nothing. Alters $self.
 Args    : None.
 Notes   :

  _get_v3_peak_indices($buffer)
 Title   : _get_v3_peak_indices($buffer)
 Usage   : $self->_get_v3_peak_indices($buffer);
 Function: Unpacks the base accuracies for version3 scf
 Returns : Nothing. Alters $self
 Args    : A scalar containing binary data.
 Notes   :

  _get_v3_base_accuracies($buffer)
 Title   : _get_v3_base_accuracies($buffer)
 Usage   : $self->_get_v3_base_accuracies($buffer)
 Function: Set the base accuracies for version 3 scf's
 Returns : Nothing. Alters $self.
 Args    : A scalar containing binary data.
 Notes   :

  _get_comments($buffer)
 Title   : _get_comments($buffer)
 Usage   : $self->_get_comments($buffer);
 Function: Gather the comments section from the scf and parse it into its
            components.
 Returns : a Bio::Annotation::Collection object
 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   :

  _get_header()
 Title   : _get_header($buffer)
 Usage   : $self->_get_header($buffer);
 Function: Gather the header section from the scf and parse it into its
           components.
 Returns : Reference to a hash containing the header components.
 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.

  _parse_v2_bases($buffer)
 Title   : _parse_v2_bases($buffer)
 Usage   : $self->_parse_v2_bases($buffer);
 Function: Gather the bases section from the scf and parse it into its
           components.
 Returns :
 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.

  _parse_v2_traces(\@traces_array)
 Title   : _pares_v2_traces(\@traces_array)
 Usage   : $self->_parse_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_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   :

  get_comments()
 Title   : get_comments()
 Usage   : %comments = %{$obj->get_comments()};
 Function: Return the comments for this scf.
 Returns : A Bio::Annotation::Collection object
 Args    : None.
 Notes   :

  write_seq
 Title   : write_seq(-target => $swq, <comments>)
 Usage   : $obj->write_seq(
               -target => $swq,
            -version => 2,
            -CONV => "Bioperl-Chads Mighty SCF writer.");
 Function: Write out an scf.
 Returns : Nothing.
 Args    : Requires: a reference to a Bio::Seq::Quality 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   :
          For best results, use a SequenceTrace object.
          The things that you need to write an scf:
          a) sequence
          b) quality
          c) peak indices
          d) traces
          - You _can_ write an scf with just a and b by passing in a
               Bio::Seq::Quality object- false traces will be synthesized
               for you.

  _get_binary_header()
 Title   : _get_binary_header();
 Usage   : $self->_get_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   :

  _get_binary_traces($version,$ref)
 Title   : _set_binary_tracesbases($version,$ref)
 Usage   : $self->_set_binary_tracesbases($version,$ref);
 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 - a reference to either a SequenceTraces or a
          SequenceWithQuality object.
 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   :

  _get_binary_comments(\@comments)
 Title   : _get_binary_comments(\@comments)
 Usage   : $self->_get_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 :
 Args    : A reference to an array containing comments.
 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.