Package: mafft
Version: 6.240-1
Filename: pool/main/m/mafft/mafft_6.240-1_i386.deb


Found error in /usr/bin/mafft-homologs:
	$ grep -A5 -B5 /tmp/ /usr/bin/mafft-homologs
	#             (default: well-aligned region only)
	
	
	require 'getopts'
	
	system( mafftpath + " --help > /tmp/_vf#{$$} 2>&1" )
	pfp = File.open( "/tmp/_vf#{$$}", 'r' )
	while pfp.gets
		break if $_ =~ /MAFFT v/
	end
	pfp.close
	if( $_ ) then
	--
	end
	if $OPT_o then
		mafftopt += " " + $OPT_o + " "
	end
	
	system "cat " + ARGV.to_s + " > /tmp/_if#{$$}"
	ar = mafftopt.split(" ")
	nar = ar.length
	for i in 0..(nar-1)
		if ar[i] == "--seed" then
			system "cat #{ar[i+1]} >> /tmp/_if#{$$}"
		end
	end
	
	nseq = 0
	ifp = File.open( "/tmp/_if#{$$}", 'r' )
		while ifp.gets
			nseq += 1 if $_ =~ /^>/
		end
	ifp.close
	
	STDERR.puts "Performing preliminary alignment .. "
	if nseq == 1 then
		system( "cp /tmp/_if#{$$}"  + " /tmp/_pf#{$$}" )
	else
		if entiresearch == 1 then
	#		system( mafftpath + " --maxiterate 1000 --localpair /tmp/_if#{$$} > /tmp/_pf#{$$}" )
			system( mafftpath + " --maxiterate 0 --retree 2 /tmp/_if#{$$} > /tmp/_pf#{$$}" )
		else
			system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} /tmp/_if#{$$} > /tmp/_pf#{$$}" )
		end
	end
	
	pfp = File.open( "/tmp/_pf#{$$}", 'r' )
	inname = []
	inseq = []
	slen = []
	act = []
	nin = 0
	--
		slen.push( inseq[i].gsub(/-/,"").length )
		act.push( 1 )
	end
	pfp.close
	
	pfp = File.open( "/tmp/_if#{$$}", 'r' )
	orname = []
	orseq = []
	nin = 0
	nin = readfasta( pfp, orname, orseq )
	pfp.close
	--
		end
	end
	#p act
	
	
	afp = File.open( "/tmp/_af#{$$}", 'w' )
	
	STDERR.puts "Searching .. \n"
	ids = []
	add = []
	sco = []
	--
			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' > /tmp/_rid#{$$}"
			system command
		
			ridp = File.open( "/tmp/_rid#{$$}", 'r' )
			while ridp.gets
				break if $_ =~ / RID = (.*)/
			end
			ridp.close
			rid = $1.strip
	--
		
			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' > /tmp/_res#{$$}"
				system command
				resp = File.open( "/tmp/_res#{$$}", 'r' )
	#			resp.gets
	#			if $_ =~ /WAITING/ then
	#				resp.close
	#				next
	#			end
	--
				end
			end
		else
	#		puts "Not supported"
	#		exit
			qfp = File.open( "/tmp/_q#{$$}", 'w' )
				qfp.puts "> "
				qfp.puts inseq[i]
			qfp.close
			command = blastpath + "  -p blastp  -e #{eval} -b 1000 -m 7 -i /tmp/_q#{$$} -d #{localdb} > /tmp/_res#{$$}"
			system command
			resp = File.open( "/tmp/_res#{$$}", 'r' )
		end
		STDERR.puts " Done.\n\n"
	
		resp = File.open( "/tmp/_res#{$$}", 'r' )
		while 1
			while resp.gets
				break if $_ =~ /<Hit_id>(.*)<\/Hit_id>/ || $_ =~ /(<Iteration_stat>)/
			end
			id = $1
	--
		outnum += 1
	end
	afp.close
	
	STDERR.puts "Performing alignment .. "
	system( mafftpath + mafftopt + " /tmp/_af#{$$} > /tmp/_bf#{$$}" )
	STDERR.puts "done."
	
	bfp = File.open( "/tmp/_bf#{$$}", 'r' )
	outseq = []
	outnam = []
	readfasta( bfp, outnam, outseq )
	bfp.close
	
	--
	for i in 0..(nout-1)
		puts ">" + outnam2[i]
		puts outseq2[i].gsub( /.{1,60}/, "\\0\n" )
	end
	
	system( "rm -rf /tmp/_if#{$$} /tmp/_vf#{$$} /tmp/_af#{$$} /tmp/_bf#{$$} /tmp/_pf#{$$} /tmp/_q#{$$} /tmp/_res#{$$} /tmp/_rid#{$$}" )