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)