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bio::seqio::strider(3pm) [debian man page]

Bio::SeqIO::strider(3pm)				User Contributed Perl Documentation				  Bio::SeqIO::strider(3pm)

NAME

       Bio::SeqIO::strider - DNA strider sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::SeqIO class.

DESCRIPTION

       This object can transform Bio::Seq objects to and from strider 'binary' format, as documented in the strider manual, in which the first 112
       bytes are a header, following by the sequence, followed by a sequence description.

       Note: it does NOT assign any sequence identifier, since they are not contained in the byte stream of the file; the Strider application
       simply displays the name of the file on disk as the name of the sequence. The caller should set the id, probably based on the name of the
       file (after possibly cleaning up whitespace, which ought not to be used as the id in most applications).

       Note: the strider 'comment' is mapped to the BioPerl 'description' (since there is no other text field, and description maps to defline
       text).

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://redmine.open-bio.org/projects/bioperl/

AUTHORS - Malcolm Cook
       Email: mec@stowers-institute.org

CONTRIBUTORS

       Modelled after Bio::SeqIO::fasta by Ewan Birney <birney@ebi.ac.uk> and Lincoln Stein <lstein@cshl.org>

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	: $seq = $stream->next_seq()
	Function: returns the next sequence in the stream
	Returns : Bio::Seq object
	Args	: NONE

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq(@seq)
	Function: writes the $seq object into the stream
	Returns : 1 for success and 0 for error
	Args	: array of 1 to n Bio::PrimarySeqI objects

perl v5.14.2							    2012-03-02						  Bio::SeqIO::strider(3pm)

Check Out this Related Man Page

Bio::SeqIO::ace(3pm)					User Contributed Perl Documentation				      Bio::SeqIO::ace(3pm)

NAME

       Bio::SeqIO::ace - ace sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::SeqIO class.

DESCRIPTION

       This object can transform Bio::Seq objects to and from ace file format.	It only parses a DNA or Peptide objects contained in the ace file,
       producing PrimarySeq objects from them.	All other objects in the files will be ignored.  It doesn't attempt to parse any annotation
       attatched to the containing Sequence or Protein objects, which would probably be impossible, since everyone's ACeDB schema can be
       different.

       It won't parse ace files containing Timestamps correctly either.  This can easily be added if considered necessary.

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://redmine.open-bio.org/projects/bioperl/

AUTHORS - James Gilbert
       Email: jgrg@sanger.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	: $seq = $stream->next_seq()
	Function: returns the next sequence in the stream
	Returns : Bio::Seq object
	Args	: NONE

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq(@seq)
	Function: writes the $seq object into the stream
	Returns : 1 for success and 0 for error
	Args	: Bio::Seq object(s)

perl v5.14.2							    2012-03-02						      Bio::SeqIO::ace(3pm)
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