| Bio::Tools::Run::Seg(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Seg(3pm) |
Bio::Tools::Run::Seg - Object for identifying low complexity
regions in a given protein seequence.
# Build a Seg factory
# $paramfile is the full path to the seg binary file
my @params = ('PROGRAM',$paramfile);
my $factory = Bio::Tools::Run::Seg->new($param);
# Pass the factory a Bio::Seq object
# @feats is an array of Bio::SeqFeature::Generic objects
my @feats = $factory->run($seq);
Seg is a program which identifies low complexity regions in proteins. It was developed by Wootton and Federhen at NCBI.
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Please direct usage questions or support issues to the mailing list:
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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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns : string, or undef if $SEGDIR not in ENV Args : None
Title : new Usage : $rm->new(@params) Function: creates a new Seg factory Returns: Bio::Tools::Run::Seg Args :
Title : predict_protein_features() Usage : DEPRECATED Use $obj->run($seq) instead Function: Runs Seg and creates an array of featrues Returns : An array of Bio::SeqFeature::Generic objects Args : A Bio::PrimarySeqI
Title : run Usage : $obj->run($seq) Function: Runs Seg and creates an array of featrues Returns : An array of Bio::SeqFeature::Generic objects Args : A Bio::PrimarySeqI
Title : _input Usage : obj->_input($seqFile) Function: Internal (not to be used directly) Returns : Args :
Title : _run Usage : $obj->_run() Function: Internal (not to be used directly) Returns : An array of Bio::SeqFeature::Generic objects Args : None
Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal (not to be used directly) Returns : string - Fasta filename to which $seq was written Args : Bio::Seq object
| 2018-09-14 | perl v5.26.2 |