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