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BioPerl-1.7.8
River stage two • 60 direct dependents • 64 total dependents
/ Bio::SeqIO::fasta

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

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

next_seq_fast


            

              
              
Title   : next_seq_fast
Usage   : $seq = $stream->next_seq_fast()
Function: returns the next sequence in the stream
          Favors speed over perfection.
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 (not counting whitespace).
Returns : value of width
Args    : newvalue (optional)

block


            

              
              
Title   : block
Usage   : $obj->block($newval)
Function: Get/Set the length of each block for FASTA output. Sequence blocks
          will be split with a space. Configuring block, to a value of 10 for
          example, allows one to easily identify a position in a sequence by eye.
Default : same value used for width.
Returns : value of block
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 : 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.