12-04-2006
hi vino,
I don't find any grep -o option. can anyone give me UNIX code as python is not available in our development server.
Thanks in advance
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LEARN ABOUT DEBIAN
tfbs::patterngen::elph
TFBS::PatternGen::Elph(3pm) User Contributed Perl Documentation TFBS::PatternGen::Elph(3pm)
NAME
TFBS::PatternGen::Elph - a pattern factory that uses the Elph program
SYNOPSIS
my $patterngen =
TFBS::PatternGen::Elph->new(-seq_file=>'sequences.fa',
-binary => '/Elph/elph'
-motif_length => [8, 9, 10],
-additional_params => '-x -r -e');
my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
DESCRIPTION
TFBS::PatternGen::Gibbs builds position frequency matrices using an advanced Gibbs sampling algorithm implemented in external Gibbs program
by Chip Lawrence. The algorithm can produce multiple patterns from a single set of sequences.
new
Title : new
Usage : my $db = TFBS::PatternGen::Gibbs->new(%args);
Function: the constructor for the TFBS::PatternGen::Gibbs object
Returns : a TFBS::PatternGen::Gibbs object
Args : This method takes named arguments;
you must specify one of the following three
-seq_list # a reference to an array of strings
# and/or Bio::Seq objects
# or
-seq_stream # A Bio::SeqIO object
# or
-seq_file # the name of the fasta file containing
# all the sequences
Other arguments are:
-binary # a fully qualified path to Gibbs executable
# OPTIONAL: default 'Gibbs'
-nr_hits # a presumed number of pattern occurences in the
# sequence set: it can be a single integer, e.g.
# -nr_hits => 24 , or a reference to an array of
# integers, e.g -nr_hits => [12, 24, 36]
-motif_length # an expected length of motif in nucleotides:
# it can be a single integer, e.g.
# -motif_length => 8 , or a reference to an
# array ofintegers, e.g -motif_length => [8..12]
-additional_params # a string containing additional
# command-line switches for the
# Gibbs program
pattern
all_patterns
patternSet
The three methods listed above are used for the retrieval of patterns, and are common to all TFBS::PatternGen::* classes. Please see
TFBS::PatternGen for details.
perl v5.14.2 2008-01-24 TFBS::PatternGen::Elph(3pm)