Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data
# get a FastaHSP from a SearchIO stream my $in = new Bio::SearchIO(-format => 'fasta', -file => 'filename.fasta'); while( my $r = $in->next_result) { while( my $hit = $r->next_result ) { while( my $hsp = $hit->next_hsp ) { print "smith-waterman score (if available): ", $hsp->sw_score(),"\n"; } } }
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::Search::HSP::FastaHSP(); Function: Builds a new Bio::Search::HSP::FastaHSP object Returns : Bio::Search::HSP::FastaHSP Args : -swscore => smith-waterman score
Title : sw_score Usage : $obj->sw_score($newval) Function: Get/Set Smith-Waterman score Returns : value of sw_score Args : newvalue (optional)
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.