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bio::searchio::cross_match(3pm) [debian man page]

Bio::SearchIO::cross_match(3pm) 			User Contributed Perl Documentation			   Bio::SearchIO::cross_match(3pm)

NAME
Bio::SearchIO::cross_match - CrossMatch-specific subclass of Bio::SearchIO SYNOPSIS
# Working with iterations (CrossMatch results) my $searchIO = Bio::SearchIO->new( -format => 'cross_match', -file => "$file.screen.out" ) while(my $r = $searchIO->next_result) { while(my $hit = $r->next_hit) { while(my $hsp = $hit->next_hsp) { #Do the processing here. } } } # See Bio::SearchIO for information about working with Results. # See Bio::SearchIO # for details about working with Bio::SearchIO. DESCRIPTION
This object is a subclass of Bio::SearchIO and provides some operations that facilitate working with CrossMatch and CrossMatch results. For general information about working with Results, see Bio::Search::Result::GenericResult. 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://redmine.open-bio.org/projects/bioperl/ AUTHOR - Shin Leong Email sleong@watson.wustl.edu CONTRIBUTORS
Additional contributors names and emails here APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_result Title : next_result Usage : $result = stream->next_result Function: Reads the next ResultI object from the stream and returns it. Certain driver modules may encounter entries in the stream that are either misformatted or that use syntax not yet understood by the driver. If such an incident is recoverable, e.g., by dismissing a feature of a feature table or some other non-mandatory part of an entry, the driver will issue a warning. In the case of a non-recoverable situation an exception will be thrown. Do not assume that you can resume parsing the same stream after catching the exception. Note that you can always turn recoverable errors into exceptions by calling $stream->verbose(2) (see Bio::Root::RootI POD page). Returns : A Bio::Search::Result::ResultI object Args : n/a See Bio::Root::RootI _alignment Title : _alignment Usage : private _parse Title : _parse Usage : private result_count Title : result_count Usage : $num = $stream->result_count; Function: Gets the number of CrossMatch results that have been parsed. Returns : integer Args : none Throws : none perl v5.14.2 2012-03-02 Bio::SearchIO::cross_match(3pm)

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Bio::SearchIO::hmmer_pull(3pm)				User Contributed Perl Documentation			    Bio::SearchIO::hmmer_pull(3pm)

NAME
Bio::SearchIO::hmmer_pull - A parser for HMMER output 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(), " "; while (my $hit = $result->next_hit) { print $hit->name(), " "; while (my $hsp = $hit->next_hsp) { print "length is ", $hsp->length(), " "; } } } 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. 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://redmine.open-bio.org/projects/bioperl/ AUTHOR - Sendu Bala Email bix@sendu.me.uk 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 perl v5.14.2 2012-03-02 Bio::SearchIO::hmmer_pull(3pm)
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