- AUTHOR - Stefan Kirov
Bio::Matrix::PSM::IO::masta - motif fasta format parser
MASTA is a position frequency matrix format similar to fasta. It contains one ID row just like fasta and then the actual data, which is tab delimited:
0.1 0.62 .017 0.11 0.22 0.13 0.54 0.11
Or A,C,G and T could be horizontally positioned (positioning is automatically detected). Please note masta will parse only DNA at the moment.
It will also convert a set of aligned sequences: ACATGCAT ACAGGGAT ACAGGCAT ACCGGCAT
to a PFM (SiteMatrix object). When writing if you supply SEQ it will write 10 random instances, which represent correctly the frequency and can be used as an input for weblogo creation purposes.
See Bio::Matrix::PSM::IO for detailed documentation on how to use masta parser
Parser for meme.
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
AUTHOR - Stefan Kirov
Title : new Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=> 'masta', -file => $file, -mtype => 'PWM'); Function: Associates a file with the appropriate parser Throws : Example : Args : hash Returns : "Bio::Matrix::PSM::$format"->new(@args);
Title : write_psm Usage : Function: writes a pfm/pwm/raw sequence in a simple masta format Throws : Example : Args : SiteMatrix object, type (optional string: PWM, SEQ or PFM) Returns :
Title : next_matrix Usage : my $matrix = $psmio->next_matrix; Function: Alias of next_psm function
Title : next_psm Usage : my $matrix=$psmio->next_psm; Function: returns the next matrix in the stream Throws : If there is you mix different types, for example weights and frequencies occur in the same entry You can mix weights, but these should be designated by different ID lines Example : Args : Returns : Bio::Matrix::PSM::SiteMatrix