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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
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 )
# 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]
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] )
next
end
outseq2.push( outseq[i] )
- outnam2.push( outnam[i].sub( /^_addedbymaffte_/, "_ho_" ) )
+ outnam2.push( outnam[i].sub( /_addedbymaffte_/, "_ho_" ) )
end
nout = outseq2.length
end
nout = outseq2.length