| Bio::Tools::Seg(3pm) | User Contributed Perl Documentation | Bio::Tools::Seg(3pm) |
Bio::Tools::Seg - parse "seg" output
use Bio::Tools::Seg;
my $parser = Bio::Tools::Seg->(-file => 'seg.fasta');
while ( my $f = $parser->next_result ) {
if ($f->score < 1.5) {
print $f->location->to_FTstring, " is low complexity\n";
}
}
"seg" identifies low-complexity regions on a protein sequence. It is usually part of the "WU-BLAST" and "InterProScan" packages.
The Bio::Tools::Seg module will only parse the "fasta" output modes of "seg", i.e. "seg -l" (low complexity regions only), "seg -h" (high complexity regions only), or "seg -a" (both low and high).
It creates a Bio::SeqFeature::Generic for each FASTA-like entry found in the input file. It is up to the user to appropriately filter these using the feature's score.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
Email - torsten.seemann AT infotech.monash.edu.au
Email - savikalpa@fugu-sg.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::Tools::Seg->new(); Function: Builds a new Bio::Tools::Seg object Returns : Bio::Tools::Seg Args : -fh/-file => $val, # for initing input, see Bio::Root::IO
Title : next_result Usage : my $feat = $seg->next_result Function: Get the next result set from parser data Returns : Bio::SeqFeature::Generic Args : none
| 2020-10-28 | perl v5.30.3 |