A number of programs won't handle sequences with gaps or ambiguous characters. This then is a script that reports those problems (e.g. telling you the problem is at residue x in sequence y)and can optionally patch it with the consensus sequence at that location.

check_alignments_ambiguous_characters.rb

#!/usr/bin/env ruby
# Check alignment for gaps or ambiguous characters and possibly fix them.

### IMPORTS

require 'bio'
require 'test/unit/assertions'
require 'optparse'
require 'pp'

include Test::Unit::Assertions


### IMPLEMENTATION

def each_match (str, re, &block)
str.scan(re) {
block.call($~)
}
end

# Check a sequence for unclear characters
#
def check_seq(seq)
seq_str = seq.to_str.downcase()
puts "= Checking #{seq.entry_id} ..."
"Length: #{seq.length}"

#illegal_chars = seqdata.split(//).uniq() - %w[a c g t A C G T]
#if (0 < illegal_chars.length)
#  puts "#{title} has ambigs or gaps '#{illegal_chars.join()}' ..."
#end

probs = []
each_match(seq_str, /[^\-acgt]+/) { |m| probs << m }
if (0 < probs.length)
puts "= #{seq.entry_id} has has ambigs or gaps ..."
probs.each { |m|
puts "- '#{m[0]}' at #{m.offset(0)[0]}-#{m.offset(0)[1]}"
}
end
return probs

end


### MAIN

# Parse commandline arguments.
#
def parse_clargs(arg_arr)
clopts = {
:repair_with_conc => false,
:overwrite => false,
}
OptionParser.new { |opts|
opts.banner = "Usage: checkseqs.rb [options] <seqfile1> [seqfile2] ..."

opts.on('-h', '--help', 'Display this screen') {
puts opts
exit
}
opts.on('', '--repair-with-conc',
"'Repair' any ambiguous sites with the consensus sequence and save results") {
clopts[:repair_with_conc] = true
}
opts.on('', '--overwrite',
"If saving output, overwrite pre-existing files") {
clopts[:overwrite] = true
}
#opts.on("-v", "--[no-]verbose", "Run verbosely") { |v|
#	options[:verbose] = v
#}
opts.parse!()
}

pargs = ARGV
assert(0 < pargs.length, "need at least one file to work on")

return clopts, pargs
end

# Main script functionality.
#
def main()
clopts, infiles = parse_clargs(ARGV)

infiles.each { |f|
puts "== Checking file #{f} ..."

# gather and report sequence problems
all_seqs = []
seq_probs = {}
Bio::FlatFile.auto(f) { |rec|
rec.each { |entry|
seq = entry.to_seq()
all_seqs << seq
probs = check_seq(seq)
if (0 < probs.length)
seq_probs[seq] = probs
end
}
}

# correct seq if requested
if (clopts[:repair_with_conc])
# generate conc
aln = Bio::Alignment.new(all_seqs)
conc = aln.consensus_string(0.5, :gap_mode=>-1)

# repair seqs
all_seqs.each { |s|
probs = seq_probs.fetch(s, nil)
if probs
probs.each { |m|
offset = m.offset(0)
s[offset[0]...offset[1]] = conc[offset[0]...offset[1]]
}
end
}

outpath = File.basename(f, File.extname(f)) + ".clean.fasta"
if clopts[:overwrite]
assert(! File.exists?(outpath))
end

hndl = File.open(outpath, 'wb')
all_seqs.each { |s|
hndl.write(s.output())
}
hndl.close()

end

}
puts "Finished."
end

if $0 == __FILE__
main()
end


### END