Bio::Matrix::PSM::IO::masta man page on Fedora

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Bio::Matrix::PSM::IO::UseraContributed Perl DocuBio::Matrix::PSM::IO::masta(3)

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:

	 http://bugzilla.open-bio.org/

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

perl v5.14.1			  2011-07-22	Bio::Matrix::PSM::IO::masta(3)
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