bio-jaspar

require 'bio-jaspar'

# Substitute the database credentials!
db = Bio::Jaspar::JASPAR5.new(
	:host => <db_host.org>,
	:name => <db_name>,
	:user => <db_user>,
	:password => <db_password>
)

m = db.fetch_motif_by_id("MA0049")
puts m.to_s

motifs = db.fetch_motifs(
	:collection => "CORE",
	:tax_group => ["fungi", "vertebrate"],
	:tf_class => "Helix-Turn-Helix",
	:min_ic => 2
)
motifs.each { |m| # do something with a motif }

m = db.fetch_motif_by_id("MA0049")

# Consensus sequence
m.consensus 					# BioRuby Sequence object
puts m.consensus

# Anticonsensus sequence
m.anticonsensus				# BioRuby Sequence object
puts m.anticonsensus

# Reverse complement motif
m.reverse_complement	# Bio::Motif::Motifs object

# Pseudocounts
m.pseudocounts

# Background
m.background

# Position weight matrix
m.pwm

# Position specific scoring matrix
m.pssm

m = db.fetch_motif_by_id("MA0049")

# Maximum possible score for the given motif
m.pssm.max

# Minimum possible score for the given motif
m.pssm.min

# Expected value of the motif score
m.pssm.mean

# Standard deviation of the given motif score
m.pssm.std

# Find hits with the PWM score above given threshold
m.pssm.search(Bio::Sequence.auto("ACCTGCCTAAAAAA"), threshold = 0.5)

# Read a pfm file
f = File.open("test.pfm", "r")
Bio::Jaspar.read(f, "pfm")
f.close

# Write motifs into a jaspar file
motifs = db.fetch_motifs(
	:collection => "CORE",
	:tax_group => ["fungi", "vertebrate"],
	:tf_class => "Helix-Turn-Helix",
	:min_ic => 2
)
File.open("test.jaspar", "w") do |f|
	Bio::Jaspar.write(f, "jaspar")
end