Bio::SearchIO::cross_match(3) CrossMatch-specific subclass of Bio::SearchIO


# 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.


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.


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  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

[email protected]

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:

AUTHOR - Shin Leong

Email [email protected]


Additional contributors names and emails here


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 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


 Title   : _alignment
 Usage   : private


 Title   : _parse
 Usage   : private


 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