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 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://github.com/bioperl/bioperl-live/issues
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