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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)

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

NAME
Bio::SeqIO::fasta - fasta 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 fasta flat file databases. 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 - Ewan Birney &; Lincoln Stein Email: birney@ebi.ac.uk lstein@cshl.org CONTRIBUTORS
Jason Stajich, jason-at-bioperl.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, or nothing if no more available 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 or more Bio::PrimarySeqI objects width Title : width Usage : $obj->width($newval) Function: Get/Set the line width for FASTA output Returns : value of width Args : newvalue (optional) preferred_id_type Title : preferred_id_type Usage : $obj->preferred_id_type('accession') Function: Get/Set the preferred type of identifier to use in the ">ID" position for FASTA output. Returns : string, one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES. Default = $Bio::SeqIO::fasta::DEFAULT_SEQ_ID_TYPE ('display'). Args : string when setting. This must be one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values: accession, accession.version, display, primary Throws : fatal exception if the supplied id type is not in @SEQ_ID_TYPES. perl v5.14.2 2012-03-02 Bio::SeqIO::fasta(3pm)
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