NAME¶
Bio::Matrix::PSM::IO::masta - motif fasta format parser
SYNOPSIS¶
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
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=> 'masta',
-file => $file,
-mtype => 'PWM');
Function: Associates a file with the appropriate parser
Throws :
Example :
Args : hash
Returns : "Bio::Matrix::PSM::$format"->new(@args);
write_psm¶
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 :
next_matrix¶
Title : next_matrix
Usage : my $matrix = $psmio->next_matrix;
Function: Alias of next_psm function
next_psm¶
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