NAME¶
Bio::Matrix::PSM::IO::meme - PSM meme parser implementation
SYNOPSIS¶
See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers
DESCRIPTION¶
Parser for meme.
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://github.com/bioperl/bioperl-live/issues
AUTHOR - Stefan Kirov¶
Email skirov@utk.edu
APPENDIX¶
new¶
Title : new
Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme',
-file=>$file);
Function: Associates a file with the appropriate parser
Throws : Throws if the file passed is in HTML format or
if the MEME header cannot be found.
Example :
Args : hash
Returns : "Bio::Matrix::PSM::$format"->new(@args);
_parse_coordinates¶
Title : _parse_coordinates
Usage :
Function:
Throws :
Example : Internal stuff
Returns :
Args :
Title : header
Usage : my %header=$psmIO->header;
Function: Returns the header for the MEME file
Throws :
Example : Fetching all the sequences included in the MEME analysis,
being parsed
my %header=$psmIO->header;
foreach my $seqid (@{$header{instances}}) {
my $seq=$db->get_Seq_by_acc($id);
#Do something with the sequence
}
where $db might be Bio::DB:GenBank object, see
Returns : Hash with three keys: instances, weights and lengths, which
should be self-explenatory. Each value is an array
reference. Each array element corresponds to the same
element in the other two arrays. So $header{instances}->[$i]
will refer to the same sequence in the motif file as
$header{weights}->[$i] and $header{lengths}->[$i]
Args : none
Notes : OBSOLETE!
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 : Throws if the format is inconsistent with the rules for MEME 3.0.4:
no SUMMARY Section present or some keywords are missing/altered.
Example :
Returns : Bio::Matrix::PSM::Psm object
Args : none
_parseMatrix¶
Title : _parseMatrix
Usage :
Function: Parses the next site matrix information in the meme file
Throws :
Example : Internal stuff
Returns : hash as for constructing a SiteMatrix object (see SiteMatrixI)
Args : string
_parse_logs¶
Title : _parse_logs
Usage :
Function: Parses the next site matrix log values in the meme file
Throws :
Example : Internal stuff
Returns : array of array refs
Args : string
_parseInstance¶
Title : _parseInstance
Usage :
Function: Parses the next sites instances from the meme file
Throws :
Example : Internal stuff
Returns : Bio::Matrix::PSM::InstanceSite object
Args : none