SYNOPSIS
# do not use this class directly it is available through Bio::SearchIO
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
-file => 't/data/hmmpfam.bigout');
while (my $result = $in->next_result) {
# this is a Bio::Search::Result::HmmpfamResult object
print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
while (my $hit = $result->next_hit) {
print $hit->name(), "\n";
while (my $hsp = $hit->next_hsp) {
print "length is ", $hsp->length(), "\n";
}
}
}
DESCRIPTION
This object implements a pull-parser for HMMER output. It is fast since it only does work on request (hence 'pull').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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 - Sendu Bala
Email [email protected]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::SearchIO::hmmer_pull->new(); Function: Builds a new Bio::SearchIO::hmmer_pull object Returns : Bio::SearchIO::hmmer_pull Args : -fh/-file => HMMER output filename -format => 'hmmer_pull' -evalue => float or scientific notation number to be used as an evalue cutoff for hits -score => integer or scientific notation number to be used as a score value cutoff for hits -hsps => integer minimum number of hsps (domains) a hit must have -piped_behaviour => 'temp_file'|'memory'|'sequential_read' -piped_behaviour defines what the parser should do if the input is an unseekable filehandle (eg. piped input), see Bio::PullParserI::chunk for details. Default is 'sequential_read'.
next_result
Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none
result_count
Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed. Returns : integer Args : none
rewind
Title : rewind Usage : $searchio->rewind; Function: Allow one to reset the Result iterator to the beginning, so that next_result() will subsequently return the first result and so on. NB: result objects are not cached, so you will get new result objects each time you rewind. Also, note that result_count() counts the number of times you have called next_result(), so will not be able tell you how many results there were in the file if you use rewind(). Returns : n/a Args : none