Christopher Fields > BioPerl-1.6.921 > Bio::Matrix::PSM::IO::psiblast

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Module Version: 1.006921   Source   Latest Release: BioPerl-1.6.924

NAME ^

Bio::Matrix::PSM::IO::psiblast - PSM psiblast parser

SYNOPSIS ^

See Bio::Matrix::PSM::IO for documentation

DESCRIPTION ^

Parser for ASCII matrices from PSI-BLAST (blastpgp program in BLAST distribution).

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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - James Thompson ^

Email tex@biosysadmin.com

APPENDIX ^

new

 Title   : new
 Usage   : my $psmIO  =  Bio::Matrix::PSM::IO->new(-format=>'psiblast', 
                                                  -file=>$file);
 Function: Associates a file with the appropriate parser
 Throws  :
 Example :
 Args    :
 Returns : Bio::Matrix::PSM::ProtMatrix->new(@args);

next_psm

 Title   : next_psm
 Usage   : my $psm = $psmIO->next_psm();
 Function: Reads the next PSM from the input file, associated with this object
 Throws  : None
 Returns : Bio::Matrix::PSM::ProtPsm object
 Args    : none
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