Fix core WST file

[jabaws.git] / binaries / src / mafft / core / mafft-homologs.tmpl

diff --git a/binaries/src/mafft/core/mafft-homologs.tmpl b/binaries/src/mafft/core/mafft-homologs.tmpl
index 63a7116..c06743c 100644 (file)
--- a/binaries/src/mafft/core/mafft-homologs.tmpl
+++ b/binaries/src/mafft/core/mafft-homologs.tmpl
@@ -300,7 +300,7 @@ for i in 0..(nin-1)
                        break if $_ =~ /<Hsp_hseq>(.*)<\/Hsp_hseq>/
                end
 #              break if $1 == nil
-               target = $1.sub( /-/, "" )
+               target = $1.sub( /-/, "" ).sub( /U/, "X" )
 #              p target
 #              STDERR.puts "adding 1 seq"
                ids.push( id )
@@ -340,11 +340,11 @@ outnam2 = []
 len = outseq.length
 for i in 0..(len-1)
 #      p outnam[i]
-       if fullout == 0 && outnam[i] =~ /^_addedbymaffte_/ then
+       if fullout == 0 && outnam[i] =~ /_addedbymaffte_/ then
                next
        end
        outseq2.push( outseq[i] )
-       outnam2.push( outnam[i].sub( /^_addedbymaffte_/, "_ho_" ) )
+       outnam2.push( outnam[i].sub( /_addedbymaffte_/, "_ho_" ) )
 end
 
 nout = outseq2.length