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Contents
class Bio::NucleicAcid
IUPAC_CODES = {
'y' => 'ct',
'r' => 'ag',
'w' => 'at',
's' => 'cg',
'k' => 'gt',
'm' => 'ac',
'b' => 'cgt',
'd' => 'agt',
'h' => 'act',
'v' => 'acg',
'n' => 'acgt',
'a' => 'a',
't' => 't',
'g' => 'g',
'c' => 'c',
'u' => 'u',
'ct' => 'y',
'ag' => 'r',
'at' => 'w',
'cg' => 's',
'gt' => 'k',
'ac' => 'm',
'cgt' => 'b',
'agt' => 'd',
'act' => 'h',
'acg' => 'v',
'acgt' => 'n'
}
def self.is_unambiguous(base)
"acgtACGT".match(base)
end
def self.to_IUAPC(bases)
base = IUPAC_CODES[bases.to_s.downcase.chars.sort.uniq.join]
if base == nil
p "Invalid base! #{base}"
base = 'n' #This is a patch... as one of the scripts failed here.
end
base.upcase
end
def self.is_valid(code, base)
IUPAC_CODES[code.downcase].chars.include? base.downcase
end
end
#Monkey patching to Bio::Sequence to find snps between sequences. It assumes the
#sequences are already aligned and doesn't check if a base on the first sequence is
#valid on the second.
class Bio::Sequence
def self.snps_between(seq1, seq2)
snps=0
for i in (0..seq1.size-1)
snps += 1 if seq1[i] != seq2[i]
end
snps
end
end
class String
#Monkey patching to count how many ambiguity codes are present in the string, for Nucleic Acids
def count_ambiguities
snps=0
for i in (0..self.size-1)
snps += 1 if !Bio::NucleicAcid.is_unambiguous(self[i])
end
snps
end
#Counts how many bases are uppercase
def upper_case_count
match(/[^A-Z]*/).to_s.size
end
end
Version data entries
15 entries across 15 versions & 2 rubygems