binaries/src/mafft/core/pscoffee.tmpl

   1 #! /bin/csh -f
   2
   3 #
   4 # Edit pscoffee.tmpl, not pscoffee.
   5 #
   6
   7 cat << ENDF > _lara2pairalign
   8 #! /usr/bin/env ruby
   9
  10 gets
  11 line = gets
  12 nseq = line.to_i
  13 gets
  14
  15 seq = []
  16 len = []
  17 for i in 0..(nseq-1)
  18         line = gets
  19         seq.push( line.split(' ').slice(2).to_s )
  20         len.push( line.split(' ').slice(1).to_i )
  21         gets
  22 end
  23
  24 #p seq
  25 #p len
  26
  27 while 1
  28         line = gets
  29         mem1 = line.split(' ').slice(1).to_i - 1
  30         mem2 = line.split(' ').slice(2).to_i - 1
  31
  32 #       p mem1
  33 #       p mem2
  34
  35         gets
  36
  37         aln1 = ""
  38         aln2 = ""
  39
  40         pos1bk = len[mem1] - 1
  41         pos2bk = len[mem2] - 1
  42
  43         while 1
  44                 line = gets
  45                 pos1 = line.split(' ').slice(0).to_i - 1
  46                 pos2 = line.split(' ').slice(1).to_i - 1
  47
  48                 break if line.to_i == 0
  49
  50 #               puts "\npos = \n"
  51 #               p pos1
  52 #               p pos2
  53
  54                 next if pos1 == 0 && pos2 == 0
  55
  56                 if pos1bk > pos1 then
  57                         j = pos1bk
  58                         while j > pos1
  59 #                               puts "j1= " + j.to_s
  60                                 aln1 = seq[mem1][j..j] + aln1
  61                                 aln2 = '-' + aln2
  62                                 j -= 1
  63                         end
  64                 end
  65                 if pos2bk > pos2 then
  66                         j = pos2bk
  67                         while j > pos2
  68 #                               puts "j2= " + j.to_s
  69                                 aln1 = '-' + aln1
  70                                 aln2 = seq[mem2][j..j] + aln2
  71                                 j -= 1
  72                         end
  73                 end
  74
  75
  76                 aln1 = seq[mem1][pos1..pos1] + aln1
  77                 aln2 = seq[mem2][pos2..pos2] + aln2
  78
  79 #               puts "\nadding nuc"
  80 #               p aln1
  81 #               p aln2
  82
  83                 pos1bk = pos1-1
  84                 pos2bk = pos2-1
  85
  86 #               puts "\nposbk = \n"
  87 #               p pos1bk
  88 #               p pos2bk
  89
  90         end
  91         if pos1bk >= 0 then
  92                 j = pos1bk
  93                 while j >= 0
  94                         aln1 = seq[mem1][j..j] + aln1
  95                         aln2 = '-' + aln2
  96                         j -= 1
  97                 end
  98         end
  99         if pos2bk >= 0 then
 100                 j = pos2bk
 101                 while j >= 0
 102                         aln1 = '-' + aln1
 103                         aln2 = seq[mem2][j..j] + aln2
 104                         j -= 1
 105                 end
 106         end
 107
 108         puts ">#{mem1}"
 109         puts aln1
 110         puts ">#{mem2}"
 111         puts aln2
 112
 113
 114         break if line =~ /^!/
 115 end
 116 exit
 117
 118 ENDF
 119
 120 chmod guo+rx _lara2pairalign
 121
 122 echo "####### IN PSCOFFEE ######"
 123
 124 set fname = `echo $1 | sed 's/-in=//'`
 125 cp $fname larapairs.$$
 126 ./_lara2pairalign larapairs.$$ > larapairs
 127 rm larapairs.$$