NAME¶
Bio::Tools::Seg - parse "seg" output
SYNOPSIS¶
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";
}
}
DESCRIPTION¶
"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.
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 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
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 of the bugs
and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Torsten Seemann¶
Email - torsten.seemann AT infotech.monash.edu.au
CONTRIBUTOR - Bala¶
Email - savikalpa@fugu-sg.org
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
new¶
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
next_result¶
Title : next_result
Usage : my $feat = $seg->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args : none