source: branches/lib/GDE/MAFFT/mafft-7.055-with-extensions/core/regionalrealignment.rb

#! /usr/bin/env ruby

$MAFFTCOMMAND = '"/usr/local/bin/mafft"'
# Edit the above line to specify the location of mafft.
# $MAFFTCOMMAND = '"C:\folder name\mafft.bat"' # windows
# $MAFFTCOMMAND = '"/usr/local/bin/mafft"'     # mac or cygwin
# $MAFFTCOMMAND = '"/usr/bin/mafft"'           # linux (rpm)
# $MAFFTCOMMAND = '"/somewhere/mafft.bat"'     # all-in-one version for linux or mac

#####################################################################
#
# regionalrealignment.rb version 0.1 (2013/Jul/12)
# ruby regionalrealignment.rb setting input > output
# See http://mafft.cbrc.jp/alignment/software/regionalrealignment.html
#
#####################################################################


def readfasta( fp, name, seq )
        nseq = 0
        tmpseq = ""
        while fp.gets
                if $_ =~ /^>/ then
                        name.push( $_.sub(/>/,"").strip )
                        seq.push( tmpseq ) if nseq > 0
                        nseq += 1
                        tmpseq = ""
                else
                        tmpseq += $_.strip
                end
        end
        seq.push( tmpseq )
        return nseq
end

def resolve( tree )
        while 1
#               p tree
                tree.sub!( /\,([0-9]+):(\-?[0-9\.]+)\,([0-9]+):(\-?[0-9\.]+)/, ",XXX" )
                hit1 = $1
                hit2 = $2
                hit3 = $3
                hit4 = $4
        
#               p hit1
#               p hit2
#               p hit3
#               p hit4
        
#               puts "introduce XXX"
#               p tree
        
                break unless tree.index(/XXX/)
        
                poshit = tree.index(/XXX/)
#               puts "poshit=" + poshit.to_s
        
                i = poshit
                height = 0
                while i >= 0
                        break if height == 0 && tree[i..i] == '('
                        if tree[i..i] == ')' then
                                height += 1
                        elsif tree[i..i] == '(' then
                                height -= 1
                        end
                        i -= 1
                end
        
                poskakko = i
#               puts "poskakko = " + poskakko.to_s
                zenhan = tree[0..poskakko]
                zenhan = "" if poskakko == -1
#               puts "zenhan = " + zenhan
        
                treelen = tree.length
                tree = zenhan + "(" + tree[poskakko+1..treelen]
#               puts "add ("
#               p tree
                tree.sub!( /XXX/, "#{hit1}:#{hit2}):0,#{hit3}:#{hit4}" )
        
#               p tree
end


return tree

end

if ARGV.length != 2 then
        STDERR.puts ""
        STDERR.puts "Usage: ruby #{$0} setingfile inputfile > output"
        STDERR.puts ""
        exit 1
end

infilename = ARGV[1]
tname = []
tseq = []
infp = File.open( infilename, "r" )
tin = readfasta( infp, tname, tseq )
infp.close

if tin == 0 then
                STDERR.puts ""
                STDERR.puts "Error in the '#{infilename}' file.  Is this FASTA format?\n"
                STDERR.puts ""
                exit 1
end

alnlen = tseq[0].length
if alnlen == 0 then
                STDERR.puts ""
                STDERR.puts "Error in the '#{infilename}' file.  Is this FASTA format?\n"
                STDERR.puts ""
                exit 1
end


for i in 0..(tin-1)
        if alnlen != tseq[i].length then
                STDERR.puts ""
                STDERR.puts "Please insert gaps such that all the input sequences have the same length.\n"
                STDERR.puts ""
                exit 1
        end
end

checkmap = []
for i in 0..(alnlen-1)
        checkmap.push(0)
end

outputseq = []
for i in 0..(tin-1)
        outputseq.push("")
end


settingfile = ARGV[0].to_s
reg = []
startpos = []
endpos = []
realign = []
options = []
treeoption = ""
revwarn = 0
sfp = File.open( settingfile, "r" )
while line = sfp.gets
        line.sub!(/#.*/,"")
        next if line.length < 2
        if line.strip =~ /^treeoption / then
                treeoption = line.strip.sub(/.*treeoption/,"")
                break
        end
end
sfp.close
sfp = File.open( settingfile, "r" )
while line = sfp.gets
        line.sub!(/#.*/,"")
        next if line.length < 2
        next if line.strip =~ /^treeoption/
        startposv = line.split(' ')[0].to_i - 1
        endposv = line.split(' ')[1].to_i - 1
        if startposv < 0 || endposv < 0 then
                STDERR.puts "\nError in the '#{settingfile}' file. Please check this line:\n"
                STDERR.puts line
                STDERR.puts "Sites must be numbered as 1, 2, ...\n"
                STDERR.puts "\n"
                exit 1
        end
        if startposv >= alnlen || endposv >= alnlen then
                STDERR.puts "\nError in the '#{settingfile}' file. Please check this line:\n"
                STDERR.puts line
                STDERR.puts "Sites must be numbered as 1, 2, ... #{alnlen}\n"
                STDERR.puts "\n"
                exit 1
        end
        if startposv > endposv then
                STDERR.puts "\nWarning. Please check this line:\n"
                STDERR.puts line
                STDERR.puts "Start position > End position ?\n"
                STDERR.puts "\n"
                revwarn = 1
#               exit 1
        end
        startpos.push( startposv )
        endpos.push( endposv )
        if startposv > endposv
                for k in (endposv)..(startposv)
                        checkmap[k] += 1
                end
        else
                for k in (startposv)..(endposv)
                        checkmap[k] += 1
                end
        end
        if line.split(' ')[2] == "realign"  then
                realign.push( 1 )
        elsif line.split(' ')[2] == "preserve" then
                realign.push( 0 )
        else
                STDERR.puts "\n"
                STDERR.puts "The third column must be 'realign' or 'preserve'\n"
                STDERR.puts "Please check this line:\n"
                STDERR.puts line
                STDERR.puts "\n"
                exit 1
        end
        if line =~ / \-\-/ && line =~ /realign/ then
                options.push( line.sub(/.*realign/,"").strip )
        else
                options.push( treeoption )
        end
end
sfp.close

#p startpos
#p endpos
#p options


#res = system "#{$MAFFTCOMMAND} #{treeoption} --treeout --retree 0 --thread -1 #{infilename} > _dum"
res = system "#{$MAFFTCOMMAND} #{treeoption} --treeout --retree 0  #{infilename} > _dum"

if res == false then
        STDERR.puts "\n"
        STDERR.puts "ERROR in building a guide tree"
        STDERR.puts "\n"
        exit 1
end

treefp = File.open( "#{infilename}.tree", "r" )

tree = ""
while line = treefp.gets
        tree += line.strip
        break if tree =~ /;$/
end
treefp.close

tree = tree.gsub( /_.*?:/, ":" ).gsub(/[0-9]\.[0-9]*e-[0-9][0-9]/, "0").gsub(/\[.*?\]/,"").gsub(/ /, "")
scale = 1.0
mtreefp = File.open("_tree", "w")


STDERR.puts "Tree = " +  tree

memi = [-1,-1]
leni = [-1,-1]

while tree.index( /\(/ ) 

        tree = resolve( tree )

        tree.sub!( /\(([0-9]+):(\-?[0-9\.]+),([0-9]+):(\-?[0-9\.]+)\)/, "XXX" )
        memi[0] = $1.to_i
        leni[0] = $2.to_f * scale
        memi[1] = $3.to_i
        leni[1] = $4.to_f * scale

        if leni[0] > 10 || leni[1] > 10 then
                STDERR.puts ""
                STDERR.puts "Please check the scale of branch length!"
                STDERR.puts "The unit of branch lengths must be 'substitution/site'"
                STDERR.puts "If the unit is 'substition' in your tree, please"
                STDERR.puts "use the scale argument,"
                STDERR.puts "% newick2mafft scale in > out"
                STDERR.puts "where scale = 1/(alignment length)"
                STDERR.puts ""
                exit 1
        end

#       STDERR.puts "subtree = " + $&

        if memi[1] < memi[0] then
                memi.reverse!
                leni.reverse!
        end

        tree.sub!( /XXX/, memi[0].to_s )

#       STDERR.puts "Tree = " + tree

        mtreefp.printf( "%5d %5d %10.5f %10.5f\n", memi[0], memi[1], leni[0], leni[1] )

end


mtreefp.close

numreg = startpos.length

for i in 0..(numreg-1)

        partfp = File.open( "_part", "w" )
        for j in 0..(tin-1)
                partfp.puts ">" + tname[j]
                if startpos[i] > endpos[i] then
                        partfp.puts tseq[j][endpos[i]..startpos[i]].reverse
                else
                        partfp.puts tseq[j][startpos[i]..endpos[i]]
                end
        end
        partfp.close

        if( realign[i] == 1 ) then
                STDERR.puts "Aligning region #{startpos[i]+1} - #{endpos[i]+1}"
                res = system "#{$MAFFTCOMMAND} #{options[i]} --inputorder --treein _tree _part > _partout"
                if res == false then
                        STDERR.puts "\n"
                        STDERR.puts "ERROR in aligning region #{startpos[i]+1} - #{endpos[i]+1}"
                        STDERR.puts "Please check the option:"
                        STDERR.puts "#{options[i]}"
                        STDERR.puts "\n"
                        exit 1
                end

        else
                STDERR.puts "Copying region #{startpos[i]+1} - #{endpos[i]+1}"
                system "cp _part _partout"
        end

        pname = []
        pseq = []
        partfp = File.open( "_partout", "r" )
        pin = readfasta( partfp, pname, pseq )
        partfp.close
        for j in 0..(tin-1)
                outputseq[j] += pseq[j]
        end
end

for j in 0..(tin-1)
        puts ">" + tname[j]
        puts outputseq[j]
end

STDERR.puts "Done."

numdupsites = checkmap.select{|x| x>1}.length
if numdupsites > 0 then
        STDERR.puts ""
        STDERR.puts "#########################################################"
        STDERR.puts "# Warning: #{numdupsites} sites were duplicatedly selected."
        STDERR.puts "#########################################################"
        STDERR.puts ""
end

numunselectedsites = checkmap.select{|x| x==0}.length
if numunselectedsites > 0 then
        STDERR.puts ""
        STDERR.puts "#########################################################"
        STDERR.puts "# Warning: #{numunselectedsites} sites were not selected."
        STDERR.puts "#########################################################"
        STDERR.puts ""
end

if revwarn == 1 then
        STDERR.puts ""
        STDERR.puts "#########################################################"
        STDERR.puts "# Warning: The order of sites were reversed."
        STDERR.puts "#########################################################"
        STDERR.puts ""
end


STDERR.puts ""
STDERR.puts "           Tree: computed  with #{treeoption} --treeout "
for i in 0..(numreg-1)
        range = sprintf( "%6d - %6d", startpos[i]+1, endpos[i]+1 )
        if realign[i] == 1 then
                STDERR.puts "#{range}: realigned with #{options[i]} --treein (tree)"
        else
                STDERR.puts "#{range}: preserved"
        end
end
STDERR.puts ""

File.delete( "_dum" )
File.delete( "_tree" )
File.delete( "_part" )
File.delete( "_partout" )