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.
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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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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
2018-10-27 | perl v5.26.2 |