JWS-112 Bumping version of Mafft to version 7.310.

[jabaws.git] / binaries / src / mafft / scripts / mafft-homologs.rb

diff --git a/binaries/src/mafft/scripts/mafft-homologs.rb b/binaries/src/mafft/scripts/mafft-homologs.rb
index a90e0f5..8e714e8 100644 (file)
--- a/binaries/src/mafft/scripts/mafft-homologs.rb
+++ b/binaries/src/mafft/scripts/mafft-homologs.rb
@@ -31,7 +31,8 @@ blastpath = "blastall"
 #   -w        entire sequences are subjected to BLAST search 
 #             (default: well-aligned region only)
 
-require 'getopts'
+#require 'getopts'
+require 'optparse'
 require 'tempfile'
 
 # mktemp
@@ -52,17 +53,18 @@ while pfp.gets
        break if $_ =~ /MAFFT v/
 end
 pfp.close
+
 if( $_ ) then
-       mafftversion = sub( /^\D*/, "" ).split(" ").slice(0).strip.to_s
+       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 ""
+       STDERR.puts ""
+       STDERR.puts "======================================================"
+       STDERR.puts "Install new mafft (v. >= 5.58)"
+       STDERR.puts "======================================================"
+       STDERR.puts ""
        exit
 end
 
@@ -93,40 +95,64 @@ 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
+
+#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
+params = ARGV.getopts( "sfwlhe:a:o:c:d:" )
+
+
+#if $OPT_c then
+if params["c"] != nil then
+       corewin = params["c"].to_i
 end
-if $OPT_d then
-       corethr = $OPT_d.to_f
+
+#if $OPT_d then
+if params["d"] != nil then
+       corethr = params["d"].to_f
 end
-if $OPT_w
+
+#if $OPT_w
+if params["w"] == true then
        entiresearch = 1
 end
-if $OPT_f
+
+#if $OPT_f
+if params["f"] == true then
        fullout = 1
 end
-if $OPT_s
+
+#if $OPT_s
+if params["s"] == true then
        fullout = 0
 end
-if $OPT_l
+
+#if $OPT_l
+if params["l"] == true then
        local = 1
 end
-if $OPT_e then
-       eval = $OPT_e.to_f
+
+#if $OPT_e then
+if params["e"] != nil then
+#      eval = $OPT_e.to_f
+       eval = params["e"].to_f
 end
-if $OPT_a then
-       nadd = $OPT_a.to_i
+
+#if $OPT_a then
+if params["a"] != nil then
+       nadd = params["a"].to_i
 end
-if $OPT_o then
-       mafftopt += " " + $OPT_o + " "
+
+#if $OPT_o then
+if params["o"] != nil then
+       mafftopt += " " + params["o"] + " "
 end
 
-system "cat " + ARGV.to_s + " > #{temp_if}"
+infn = ARGV[0].to_s.strip
+
+system "cat " + infn + " > #{temp_if}"
 ar = mafftopt.split(" ")
 nar = ar.length
 for i in 0..(nar-1)
@@ -224,7 +250,7 @@ for i in 0..(nin-1)
        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}"
+               command = "lynx -source 'https://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' )
@@ -239,7 +265,7 @@ for i in 0..(nin-1)
                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}"
+                       command = "lynx -source 'https://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
@@ -372,3 +398,7 @@ end
 
 
 system( "rm -rf #{temp_if} #{temp_vf} #{temp_af} #{temp_bf} #{temp_pf} #{temp_qf} #{temp_res} #{temp_rid}" )
+if File.exist?( "#{temp_af}.tree" ) then
+       system( "sed 's/_addedbymaffte_/_ho_/'  #{temp_af}.tree > #{ARGV[0].to_s}.tree" )
+       system( "rm #{temp_af}.tree" )
+end