source: tags/arb-6.0/GDE/MAFFT/mafft-7.055-with-extensions/core/mafft-homologs.tmpl

#!/usr/bin/env ruby

localdb = "sp"        
# database name from which homologues are collected 
# by locally installed blast. Leave this if you do 
# not use the '-l' option.

mafftpath = "_BINDIR/mafft"   
# path of mafft. "/usr/local/bin/mafft"
# if mafft is in your command path, "mafft" is ok.

blastpath = "blastall"   
# path of blastall. 
# if blastall is in your command path, "blastall" is ok.

# mafft-homologs.rb  v. 2.1 aligns sequences together with homologues 
# automatically collected from SwissProt via NCBI BLAST.
#
# mafft > 5.58 is required
#
# Usage:
#   mafft-homologs.rb [options] input > output
# Options:
#   -a #      the number of collected sequences (default: 50)
#   -e #      threshold value (default: 1e-10)
#   -o "xxx"  options for mafft 
#             (default: " --op 1.53 --ep 0.123 --maxiterate 1000")
#   -l        locally carries out blast searches instead of NCBI blast
#             (requires locally installed blast and a database)
#   -f        outputs collected homologues also (default: off)
#   -w        entire sequences are subjected to BLAST search 
#             (default: well-aligned region only)

require 'getopts'
require 'tempfile'

# mktemp
GC.disable
temp_vf = Tempfile.new("_vf").path
temp_if = Tempfile.new("_if").path
temp_pf = Tempfile.new("_pf").path
temp_af = Tempfile.new("_af").path
temp_qf = Tempfile.new("_qf").path
temp_bf = Tempfile.new("_bf").path
temp_rid = Tempfile.new("_rid").path
temp_res = Tempfile.new("_res").path


system( mafftpath + " --help > #{temp_vf} 2>&1" )
pfp = File.open( "#{temp_vf}", 'r' )
while pfp.gets
        break if $_ =~ /MAFFT v/
end
pfp.close
if( $_ ) then
        mafftversion = sub( /^\D*/, "" ).split(" ").slice(0).strip.to_s
else
        mafftversion = "0"
end
if( mafftversion < "5.58" ) then
        puts ""
        puts "======================================================"
        puts "Install new mafft (v. >= 5.58)"
        puts "======================================================"
        puts ""
        exit
end

srand ( 0 )

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

nadd = 50
eval = 1e-10
local = 0
fullout = 0
entiresearch = 0
corewin = 50
corethr = 0.3
mafftopt = " --op 1.53 --ep 0.123 --localpair --maxiterate 1000 --reorder "
if getopts( "s", "f", "w", "l", "h", "e:", "a:", "o:", "c:", "d:" ) == nil ||  ARGV.length == 0 || $OPT_h then
        puts "Usage: #{$0} [-h -l -e# -a# -o\"[options for mafft]\"] input_file"
        exit
end

if $OPT_c then
        corewin = $OPT_c.to_i
end
if $OPT_d then
        corethr = $OPT_d.to_f
end
if $OPT_w
        entiresearch = 1
end
if $OPT_f
        fullout = 1
end
if $OPT_s
        fullout = 0
end
if $OPT_l
        local = 1
end
if $OPT_e then
        eval = $OPT_e.to_f
end
if $OPT_a then
        nadd = $OPT_a.to_i
end
if $OPT_o then
        mafftopt += " " + $OPT_o + " "
end

system "cat " + ARGV.to_s + " > #{temp_if}"
ar = mafftopt.split(" ")
nar = ar.length
for i in 0..(nar-1)
        if ar[i] == "--seed" then
                system "cat #{ar[i+1]} >> #{temp_if}"
        end
end

nseq = 0
ifp = File.open( "#{temp_if}", 'r' )
        while ifp.gets
                nseq += 1 if $_ =~ /^>/
        end
ifp.close

if nseq >= 100 then
        STDERR.puts "The number of input sequences must be <100."
        exit
elsif nseq == 1 then
        system( "cp #{temp_if}"  + " #{temp_pf}" )
else
        STDERR.puts "Performing preliminary alignment .. "
        if entiresearch == 1 then
#               system( mafftpath + " --maxiterate 1000 --localpair #{temp_if} > #{temp_pf}" )
                system( mafftpath + " --maxiterate 0 --retree 2 #{temp_if} > #{temp_pf}" )
        else
                system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} #{temp_if} > #{temp_pf}" )
        end
end

pfp = File.open( "#{temp_pf}", 'r' )
inname = []
inseq = []
slen = []
act = []
nin = 0
nin = readfasta( pfp, inname, inseq )
for i in 0..(nin-1)
        slen.push( inseq[i].gsub(/-/,"").length )
        act.push( 1 )
end
pfp.close

pfp = File.open( "#{temp_if}", 'r' )
orname = []
orseq = []
nin = 0
nin = readfasta( pfp, orname, orseq )
pfp.close

allen = inseq[0].length
for i in 0..(nin-2)
        for j in (i+1)..(nin-1)
                next if act[i] == 0
                next if act[j] == 0
                pid = 0.0
                total = 0
                for a in 0..(allen-1)
                        next if inseq[i][a,1] == "-" || inseq[j][a,1] == "-"
                        total += 1
                        pid += 1.0 if inseq[i][a,1] == inseq[j][a,1]
                end
                pid /= total
#               puts "#{i.to_s}, #{j.to_s}, #{pid.to_s}"
                if pid > 0.5 then
                        if slen[i] < slen[j]
                                act[i] = 0 
                        else
                                act[j] = 0 
                        end
                end
        end
end
#p act


afp = File.open( "#{temp_af}", 'w' )

STDERR.puts "Searching .. \n"
ids = []
add = []
sco = []
for i in 0..(nin-1)
        inseq[i].gsub!(/-/,"")
        afp.puts ">" + orname[i]
        afp.puts orseq[i]

#       afp.puts ">" + inname[i]
#       afp.puts inseq[i]

        STDERR.puts "Query (#{i+1}/#{nin})\n" + inname[i]
        if act[i] == 0 then
                STDERR.puts "Skip.\n\n"
                next 
        end

        if local == 0 then
                command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=" + inseq[i] + "&DATABASE=swissprot&HITLIST_SIZE=" + nadd.to_s + "&FILTER=L&EXPECT='" + eval.to_s + "'&FORMAT_TYPE=TEXT&PROGRAM=blastp&SERVICE=plain&NCBI_GI=on&PAGE=Proteins&CMD=Put' > #{temp_rid}"
                system command
        
                ridp = File.open( "#{temp_rid}", 'r' )
                while ridp.gets
                        break if $_ =~ / RID = (.*)/
                end
                ridp.close
                rid = $1.strip
                STDERR.puts "Submitted to NCBI. rid = " + rid
        
                STDERR.printf "Waiting "
                while 1 
                        STDERR.printf "."
                        sleep 10
                        command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RID=" + rid + "&DESCRIPTIONS=500&ALIGNMENTS=" + nadd.to_s + "&ALIGNMENT_TYPE=Pairwise&OVERVIEW=no&CMD=Get&FORMAT_TYPE=XML' > #{temp_res}"
                        system command
                        resp = File.open( "#{temp_res}", 'r' )
#                       resp.gets
#                       if $_ =~ /WAITING/ then
#                               resp.close
#                               next
#                       end
                        while( resp.gets )
                                break if $_ =~ /QBlastInfoBegin/
                        end
                        resp.gets
                        if $_ =~ /WAITING/ then
                                resp.close
                                next
                        else
                                resp.close
                                break
                        end
                end
        else
#               puts "Not supported"
#               exit
                qfp = File.open( "#{temp_qf}", 'w' )
                        qfp.puts "> "
                        qfp.puts inseq[i]
                qfp.close
                command = blastpath + "  -p blastp  -e #{eval} -b 1000 -m 7 -i #{temp_qf} -d #{localdb} > #{temp_res}"
                system command
                resp = File.open( "#{temp_res}", 'r' )
        end
        STDERR.puts " Done.\n\n"

        resp = File.open( "#{temp_res}", 'r' )
        while 1
                while resp.gets
                        break if $_ =~ /<Hit_id>(.*)<\/Hit_id>/ || $_ =~ /(<Iteration_stat>)/
                end
                id = $1
                break if $_ =~ /<Iteration_stat>/
#               p id
                while resp.gets
                        break if $_ =~ /<Hsp_bit-score>(.*)<\/Hsp_bit-score>/
                end
                score = $1.to_f
#               p score

                known = ids.index( id )
                if known != nil then
                        if sco[known] >= score then
                                next
                        else
                                ids.delete_at( known )
                                add.delete_at( known )
                                sco.delete_at( known )
                        end
                end
                while resp.gets
                        break if $_ =~ /<Hsp_hseq>(.*)<\/Hsp_hseq>/
                end
#               break if $1 == nil
                target = $1.sub( /-/, "" ).sub( /U/, "X" )
#               p target
#               STDERR.puts "adding 1 seq"
                ids.push( id )
                sco.push( score )
                add.push( target )
        end
        resp.close
end

n = ids.length

outnum = 0
while n > 0 && outnum < nadd
        m = rand( n )
        afp.puts ">_addedbymaffte_" + ids[m]
        afp.puts add[m]
        ids.delete_at( m )
        add.delete_at( m )
        n -= 1
        outnum += 1
end
afp.close

STDERR.puts "Performing alignment .. "
system( mafftpath + mafftopt + " #{temp_af} > #{temp_bf}" )
STDERR.puts "done."

bfp = File.open( "#{temp_bf}", 'r' )
outseq = []
outnam = []
readfasta( bfp, outnam, outseq )
bfp.close

outseq2 = []
outnam2 = []

len = outseq.length
for i in 0..(len-1)
#       p outnam[i]
        if fullout == 0 && outnam[i] =~ /_addedbymaffte_/ then
                next
        end
        outseq2.push( outseq[i] )
        outnam2.push( outnam[i].sub( /_addedbymaffte_/, "_ho_" ) )
end

nout = outseq2.length
len = outseq[0].length
p = len
while p>0
        p -= 1
    allgap = 1
    for j in 0..(nout-1)
                if outseq2[j][p,1] != "-" then
                        allgap = 0
                        break
                end
    end
    if allgap == 1 then
        for j in 0..(nout-1)
            outseq2[j][p,1] = ""
        end
    end
end
for i in 0..(nout-1)
        puts ">" + outnam2[i]
        puts outseq2[i].gsub( /.{1,60}/, "\\0\n" )
end


system( "rm -rf #{temp_if} #{temp_vf} #{temp_af} #{temp_bf} #{temp_pf} #{temp_qf} #{temp_res} #{temp_rid}" )