bio 1.3.1 → 1.4.0

data/lib/bio/appl/blast/report.rb

@@ -580,7 +580,7 @@ end # Blast
 end # Bio
 
 
-if __FILE__ == $0
+#if __FILE__ == $0
 
 =begin
 
@@ -617,151 +617,6 @@ if __FILE__ == $0
 
 =end
 
-  Bio::Blast.reports(ARGF) do |rep|	# for multiple xml reports
-
-  print "# === Bio::Tools::Blast::Report\n"
-  puts
-  print "  rep.program           #=> "; p rep.program
-  print "  rep.version           #=> "; p rep.version
-  print "  rep.reference         #=> "; p rep.reference
-  print "  rep.db                #=> "; p rep.db
-  print "  rep.query_id          #=> "; p rep.query_id
-  print "  rep.query_def         #=> "; p rep.query_def
-  print "  rep.query_len         #=> "; p rep.query_len
-  puts
-
-  print "# === Parameters\n"
-  puts
-  print "  rep.parameters        #=> "; p rep.parameters
-  puts
-  print "  rep.matrix            #=> "; p rep.matrix
-  print "  rep.expect            #=> "; p rep.expect
-  print "  rep.inclusion         #=> "; p rep.inclusion
-  print "  rep.sc_match          #=> "; p rep.sc_match
-  print "  rep.sc_mismatch       #=> "; p rep.sc_mismatch
-  print "  rep.gap_open          #=> "; p rep.gap_open
-  print "  rep.gap_extend        #=> "; p rep.gap_extend
-  print "  rep.filter            #=> "; p rep.filter
-  print "  rep.pattern           #=> "; p rep.pattern
-  print "  rep.entrez_query      #=> "; p rep.entrez_query
-  puts
-
-  print "# === Statistics (last iteration's)\n"
-  puts
-  print "  rep.statistics        #=> "; p rep.statistics
-  puts
-  print "  rep.db_num            #=> "; p rep.db_num
-  print "  rep.db_len            #=> "; p rep.db_len
-  print "  rep.hsp_len           #=> "; p rep.hsp_len
-  print "  rep.eff_space         #=> "; p rep.eff_space
-  print "  rep.kappa             #=> "; p rep.kappa
-  print "  rep.lambda            #=> "; p rep.lambda
-  print "  rep.entropy           #=> "; p rep.entropy
-  puts
-
-  print "# === Message (last iteration's)\n"
-  puts
-  print "  rep.message           #=> "; p rep.message
-  puts
-
-  print "# === Iterations\n"
-  puts
-  print "  rep.itrerations.each do |itr|\n"
-  puts
-
-  rep.iterations.each do |itr|
-      
-  print "# --- Bio::Blast::Report::Iteration\n"
-  puts
-
-  print "    itr.num             #=> "; p itr.num
-  print "    itr.statistics      #=> "; p itr.statistics
-  print "    itr.message         #=> "; p itr.message
-  print "    itr.hits.size       #=> "; p itr.hits.size
-  puts
-
-  print "    itr.hits.each do |hit|\n"
-  puts
-
-  itr.hits.each do |hit|
-
-  print "# --- Bio::Blast::Report::Hit\n"
-  puts
-
-  print "      hit.num           #=> "; p hit.num
-  print "      hit.hit_id        #=> "; p hit.hit_id
-  print "      hit.len           #=> "; p hit.len
-  print "      hit.definition    #=> "; p hit.definition
-  print "      hit.accession     #=> "; p hit.accession
-
-  print "        --- compatible/shortcut ---\n"
-  print "      hit.query_id      #=> "; p hit.query_id
-  print "      hit.query_def     #=> "; p hit.query_def
-  print "      hit.query_len     #=> "; p hit.query_len
-  print "      hit.target_id     #=> "; p hit.target_id
-  print "      hit.target_def    #=> "; p hit.target_def
-  print "      hit.target_len    #=> "; p hit.target_len
-
-  print "      hit.evalue        #=> "; p hit.evalue
-  print "      hit.bit_score     #=> "; p hit.bit_score
-  print "      hit.identity      #=> "; p hit.identity
-  print "      hit.overlap       #=> "; p hit.overlap
-
-  print "      hit.query_seq     #=> "; p hit.query_seq
-  print "      hit.midline       #=> "; p hit.midline
-  print "      hit.target_seq    #=> "; p hit.target_seq
-
-  print "      hit.query_start   #=> "; p hit.query_start
-  print "      hit.query_end     #=> "; p hit.query_end
-  print "      hit.target_start  #=> "; p hit.target_start
-  print "      hit.target_end    #=> "; p hit.target_end
-  print "      hit.lap_at        #=> "; p hit.lap_at
-  print "        --- compatible/shortcut ---\n"
-
-  print "      hit.hsps.size     #=> "; p hit.hsps.size
-  puts
-
-  print "      hit.hsps.each do |hsp|\n"
-  puts
-
-  hit.hsps.each do |hsp|
-
-  print "# --- Bio::Blast::Report::Hsp\n"
-  puts
-  print "        hsp.num         #=> "; p hsp.num
-  print "        hsp.bit_score   #=> "; p hsp.bit_score 
-  print "        hsp.score       #=> "; p hsp.score
-  print "        hsp.evalue      #=> "; p hsp.evalue
-  print "        hsp.identity    #=> "; p hsp.identity
-  print "        hsp.gaps        #=> "; p hsp.gaps
-  print "        hsp.positive    #=> "; p hsp.positive
-  print "        hsp.align_len   #=> "; p hsp.align_len
-  print "        hsp.density     #=> "; p hsp.density
-
-  print "        hsp.query_frame #=> "; p hsp.query_frame
-  print "        hsp.query_from  #=> "; p hsp.query_from
-  print "        hsp.query_to    #=> "; p hsp.query_to
-
-  print "        hsp.hit_frame   #=> "; p hsp.hit_frame
-  print "        hsp.hit_from    #=> "; p hsp.hit_from
-  print "        hsp.hit_to      #=> "; p hsp.hit_to
-
-  print "        hsp.pattern_from#=> "; p hsp.pattern_from
-  print "        hsp.pattern_to  #=> "; p hsp.pattern_to
-
-  print "        hsp.qseq        #=> "; p hsp.qseq
-  print "        hsp.midline     #=> "; p hsp.midline
-  print "        hsp.hseq        #=> "; p hsp.hseq
-  puts
-  print "        hsp.percent_identity  #=> "; p hsp.percent_identity
-  print "        hsp.mismatch_count    #=> "; p hsp.mismatch_count
-  puts
-
-  end
-  end
-  end
-  end					# for multiple xml reports
-
-end
+#end
 
 

data/lib/bio/appl/blast/wublast.rb

@@ -461,211 +461,3 @@ module Bio
   end #class Blast
 end #module Bio
 
-######################################################################
-
-if __FILE__ == $0
-
-  Bio::FlatFile.open(Bio::Blast::WU::Report, ARGF) do |ff|
-  ff.each do |rep|
-
-  print "# === Bio::Blast::WU::Report\n"
-  puts
-  print "  rep.program           #=> "; p rep.program
-  print "  rep.version           #=> "; p rep.version
-  print "  rep.reference         #=> "; p rep.reference
-  print "  rep.notice            #=> "; p rep.notice
-  print "  rep.db                #=> "; p rep.db
-  #print "  rep.query_id          #=> "; p rep.query_id
-  print "  rep.query_def         #=> "; p rep.query_def
-  print "  rep.query_len         #=> "; p rep.query_len
-  #puts
-  print "  rep.version_number    #=> "; p rep.version_number
-  print "  rep.version_date      #=> "; p rep.version_date
-  puts
-
-  print "# === Parameters\n"
-  #puts
-  print "  rep.parameters        #=> "; p rep.parameters
-  puts
-  #@#print "  rep.matrix            #=> "; p rep.matrix
-  print "  rep.expect            #=> "; p rep.expect
-  #print "  rep.inclusion         #=> "; p rep.inclusion
-  #@#print "  rep.sc_match          #=> "; p rep.sc_match
-  #@#print "  rep.sc_mismatch       #=> "; p rep.sc_mismatch
-  #@#print "  rep.gap_open          #=> "; p rep.gap_open
-  #@#print "  rep.gap_extend        #=> "; p rep.gap_extend
-  #print "  rep.filter            #=> "; p rep.filter
-  #@#print "  rep.pattern           #=> "; p rep.pattern
-  #print "  rep.entrez_query      #=> "; p rep.entrez_query
-  #puts
-  #@#print "  rep.pattern_positions  #=> "; p rep.pattern_positions
-  puts
-
-  print "# === Statistics (last iteration's)\n"
-  #puts
-  #print "  rep.statistics        #=> "; p rep.statistics
-  puts
-  print "  rep.db_num            #=> "; p rep.db_num
-  print "  rep.db_len            #=> "; p rep.db_len
-  #print "  rep.hsp_len           #=> "; p rep.hsp_len
-  #@#print "  rep.eff_space         #=> "; p rep.eff_space
-  #@#print "  rep.kappa             #=> "; p rep.kappa
-  #@#print "  rep.lambda            #=> "; p rep.lambda
-  #@#print "  rep.entropy           #=> "; p rep.entropy
-  puts
-  #@#print "  rep.num_hits          #=> "; p rep.num_hits
-  #@#print "  rep.gapped_kappa      #=> "; p rep.gapped_kappa
-  #@#print "  rep.gapped_lambda     #=> "; p rep.gapped_lambda
-  #@#print "  rep.gapped_entropy    #=> "; p rep.gapped_entropy
-  #@#print "  rep.posted_date       #=> "; p rep.posted_date
-  puts
-
-  #@#print "# === Message (last iteration's)\n"
-  #@#puts
-  #@#print "  rep.message           #=> "; p rep.message
-  #puts
-  #@#print "  rep.converged?        #=> "; p rep.converged?
-  #puts
-
-  print "# === Warning messages\n"
-  print "  rep.warnings        #=> "; p rep.warnings
-
-  print "# === Iterations\n"
-  puts
-  print "  rep.itrerations.each do |itr|\n"
-  puts
-
-  rep.iterations.each do |itr|
-      
-  print "# --- Bio::Blast::WU::Report::Iteration\n"
-  puts
-
-  print "    itr.num             #=> "; p itr.num
-  #print "    itr.statistics      #=> "; p itr.statistics
-  puts
-  print "    itr.warnings        #=> "; p itr.warnings
-  print "    itr.message         #=> "; p itr.message
-  print "    itr.hits.size       #=> "; p itr.hits.size
-  #puts
-  #@#print "    itr.hits_newly_found.size    #=> "; p itr.hits_newly_found.size;
-  #@#print "    itr.hits_found_again.size    #=> "; p itr.hits_found_again.size;
-  if itr.hits_for_pattern then
-  itr.hits_for_pattern.each_with_index do |hp, hpi|
-  print "    itr.hits_for_pattern[#{hpi}].size #=> "; p hp.size;
-  end
-  end
-  print "    itr.converged?      #=> "; p itr.converged?
-  puts
-
-  print "    itr.hits.each do |hit|\n"
-  puts
-
-  itr.hits.each_with_index do |hit, i|
-
-  print "# --- Bio::Blast::WU::Report::Hit"
-  print " ([#{i}])\n"
-  puts
-
-  #print "      hit.num           #=> "; p hit.num
-  #print "      hit.hit_id        #=> "; p hit.hit_id
-  print "      hit.len           #=> "; p hit.len
-  print "      hit.definition    #=> "; p hit.definition
-  #print "      hit.accession     #=> "; p hit.accession
-  #puts
-  print "      hit.found_again?  #=> "; p hit.found_again?
-  #puts
-  print "      hit.score         #=> "; p hit.score
-  print "      hit.pvalue        #=> "; p hit.pvalue
-  print "      hit.n_number      #=> "; p hit.n_number
-
-  print "        --- compatible/shortcut ---\n"
-  #print "      hit.query_id      #=> "; p hit.query_id
-  #print "      hit.query_def     #=> "; p hit.query_def
-  #print "      hit.query_len     #=> "; p hit.query_len
-  #print "      hit.target_id     #=> "; p hit.target_id
-  print "      hit.target_def    #=> "; p hit.target_def
-  print "      hit.target_len    #=> "; p hit.target_len
-
-  print "            --- first HSP's values (shortcut) ---\n"
-  print "      hit.evalue        #=> "; p hit.evalue
-  print "      hit.bit_score     #=> "; p hit.bit_score
-  print "      hit.identity      #=> "; p hit.identity
-  #print "      hit.overlap       #=> "; p hit.overlap
-
-  print "      hit.query_seq     #=> "; p hit.query_seq
-  print "      hit.midline       #=> "; p hit.midline
-  print "      hit.target_seq    #=> "; p hit.target_seq
-
-  print "      hit.query_start   #=> "; p hit.query_start
-  print "      hit.query_end     #=> "; p hit.query_end
-  print "      hit.target_start  #=> "; p hit.target_start
-  print "      hit.target_end    #=> "; p hit.target_end
-  print "      hit.lap_at        #=> "; p hit.lap_at
-  print "            --- first HSP's vaules (shortcut) ---\n"
-  print "        --- compatible/shortcut ---\n"
-
-  puts
-  print "      hit.hsps.size     #=> "; p hit.hsps.size
-  if hit.hsps.size == 0 then
-  puts  "          (HSP not found: please see blastall's -b and -v options)"
-  puts
-  else
-
-  puts
-  print "      hit.hsps.each do |hsp|\n"
-  puts
-
-  hit.hsps.each_with_index do |hsp, j|
-
-  print "# --- Bio::Blast::WU::Report::Hsp"
-  print " ([#{j}])\n"
-  puts
-  #print "        hsp.num         #=> "; p hsp.num
-  print "        hsp.bit_score   #=> "; p hsp.bit_score 
-  print "        hsp.score       #=> "; p hsp.score
-  print "        hsp.evalue      #=> "; p hsp.evalue
-  print "        hsp.identity    #=> "; p hsp.identity
-  print "        hsp.gaps        #=> "; p hsp.gaps
-  print "        hsp.positive    #=> "; p hsp.positive
-  print "        hsp.align_len   #=> "; p hsp.align_len
-  #print "        hsp.density     #=> "; p hsp.density
-  puts
-  print "        hsp.pvalue      #=> "; p hsp.pvalue
-  print "        hsp.p_sum_n     #=> "; p hsp.p_sum_n
-  puts
-
-  print "        hsp.query_frame #=> "; p hsp.query_frame
-  print "        hsp.query_from  #=> "; p hsp.query_from
-  print "        hsp.query_to    #=> "; p hsp.query_to
-
-  print "        hsp.hit_frame   #=> "; p hsp.hit_frame
-  print "        hsp.hit_from    #=> "; p hsp.hit_from
-  print "        hsp.hit_to      #=> "; p hsp.hit_to
-
-  #print "        hsp.pattern_from#=> "; p hsp.pattern_from
-  #print "        hsp.pattern_to  #=> "; p hsp.pattern_to
-
-  print "        hsp.qseq        #=> "; p hsp.qseq
-  print "        hsp.midline     #=> "; p hsp.midline
-  print "        hsp.hseq        #=> "; p hsp.hseq
-  puts
-  print "        hsp.percent_identity  #=> "; p hsp.percent_identity
-  #print "        hsp.mismatch_count    #=> "; p hsp.mismatch_count
-  #
-  print "        hsp.query_strand      #=> "; p hsp.query_strand
-  print "        hsp.hit_strand        #=> "; p hsp.hit_strand
-  print "        hsp.percent_positive  #=> "; p hsp.percent_positive
-  print "        hsp.percent_gaps      #=> "; p hsp.percent_gaps
-  puts
-
-  end #each
-  end #if hit.hsps.size == 0
-  end
-  end
-  end #ff.each
-  end #FlatFile.open
-
-end #if __FILE__ == $0
-
-######################################################################
-

data/lib/bio/appl/fasta.rb

@@ -191,10 +191,13 @@ class Fasta
         txt.sub!(/\<\/pre\>.*\z/m, '')
         txt.sub!(/.*^((T?FASTA|SSEARCH) (searches|compares))/m, '\1')
         txt.sub!(/^\<form method\=\"POST\" name\=\"clust_check\"\>.*\n/, '')
+        txt.sub!(/^\<select +name\=\"allch\".+\r?\n/i, '') # 2009.11.26
         txt.gsub!(/\<input[^\>]+value\=\"[^\"]*\"[^\>]*\>/i, '')
         txt.gsub!(/\<(a|form|select|input|option|img)\s+[^\>]+\>/i, '')
         txt.gsub!(/\<\/(a|form|select|input|option|img)\>/i, '')
-        @output = txt.gsub(/\&lt\;/, '<')
+        txt.gsub!(/\&lt\;/, '<')
+        txt.gsub!(/\&gt\;/, '>') # 2009.11.26
+        @output = txt
         report = parse_result(@output.dup)
       else
         raise 'cannot understand response'
@@ -208,21 +211,3 @@ end # Fasta
 
 end # Bio
 
-
-if __FILE__ == $0
-  begin
-    require 'pp'
-    alias p pp
-  rescue
-  end
-
-# serv = Bio::Fasta.local('fasta34', 'hoge.nuc')
-# serv = Bio::Fasta.local('fasta34', 'hoge.pep')
-# serv = Bio::Fasta.local('ssearch34', 'hoge.pep')
-
-  # This may take 3 minutes or so.
-  serv = Bio::Fasta.remote('fasta', 'genes')
-  p serv.query(ARGF.read)
-end
-
-

data/lib/bio/appl/fasta/format10.rb

@@ -399,17 +399,3 @@ end # Report
 end # Fasta
 end # Bio
 
-
-if __FILE__ == $0
-  begin
-    require 'pp'
-    alias p pp
-  rescue
-  end
-
-  rep = Bio::Fasta::Report.new(ARGF.read)
-  p rep
-
-end
-
-

data/lib/bio/appl/genscan/report.rb

@@ -374,179 +374,3 @@ end # class Genscan
 
 end # module Bio
 
-
-
-
-
-# testing code
-
-if __FILE__ == $0
-
-  if $<.filename != '-'
-    report = $<.read
-  else
-    report = File.open(__FILE__,  'r').read.scan(/^>>>> (.+)$/).join("\n")
-  end
-
-
-  puts "= class Bio::Genscan::Report "
-  report = Bio::Genscan::Report.new(report)
-
-
-  print " report.genscan_version #=> "
-  p report.genscan_version
-  print " report.date_run #=> "
-  p report.date_run
-  print " report.time #=> "
-  p report.time
-
-  print " report.query_name #=> "
-  p report.query_name
-  print " report.length #=> "
-  p report.length
-  print " report.gccontent #=> "
-  p report.gccontent
-  print " report.isochore #=> "
-  p report.isochore
-
-  print " report.matrix #=> " 
-  p report.matrix
-
-  puts " report.predictions (Array of Bio::Genscan::Report::Gene)  " 
-  print " report.predictions.size #=> "
-  p report.predictions.size
-
-
-  report.predictions.each {|gene|
-    puts "\n== class Bio::Genscan::Report::Gene "
-    print " gene.number #=> " 
-    p gene.number
-    print " gene.aaseq (Bio::FastaFormat) #=> " 
-    p gene.aaseq
-    print " gene.naseq (Bio::FastaFormat) #=> " 
-    p gene.naseq
-    print " ene.promoter (Bio::Genscan::Report::Exon) #=> " 
-    p gene.promoter
-    print " gene.polyA (Bio::Genscan::Report::Exon) #=> " 
-    p gene.polyA
-    puts " gene.exons (Array of Bio::Genscan::Report::Exon) " 
-    print " gene.exons.size #=> " 
-    p gene.exons.size
-
-
-    gene.exons.each {|exon|
-      puts "\n== class Bio::Genscan::Report::Exon "
-      print " exon.number #=> "
-      p exon.number
-      print " exon.exon_type #=> "
-      p exon.exon_type
-      print " exon.exon_type_long #=> "
-      p exon.exon_type_long
-      print " exon.strand #=> "
-      p exon.strand
-      print " exon.first #=> "
-      p exon.first
-      print " exon.last #=> "
-      p exon.last
-      print " exon.range (Range) #=> "
-      p exon.range
-      print " exon.frame #=> "
-      p exon.frame
-      print " exon.phase #=> "
-      p exon.phase
-      print " exon.acceptor_score #=> "
-      p exon.acceptor_score
-      print " exon.donor_score #=> "
-      p exon.donor_score
-      print " exon.initiation_score #=> "
-      p exon.initiation_score
-      print " exon.termination_score #=> "
-      p exon.termination_score
-      print " exon.score #=> "
-      p exon.score
-      print " exon.p_value #=> "
-      p exon.p_value
-      print " exon.t_score #=> "
-      p exon.t_score
-      puts
-    }
-    puts
-  }
-
-end
-
-
-
-
-
-=begin
-
-
-= Sample Genscan report with '^>>>> '.
-
-
->>>> GENSCAN 1.0	Date run: 30-May-103	Time: 14:06:28
->>>> 
->>>> Sequence HUMRASH : 12942 bp : 68.17% C+G : Isochore 4 (57 - 100 C+G%)
->>>> 
->>>> Parameter matrix: HumanIso.smat
->>>> 
->>>> Predicted genes/exons:
->>>> 
->>>> Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
->>>> ----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
->>>> 
->>>>  1.01 Init +   1664   1774  111  1  0   94   83   212 0.997  21.33
->>>>  1.02 Intr +   2042   2220  179  1  2  104   66   408 0.997  40.12
->>>>  1.03 Intr +   2374   2533  160  1  1   89   94   302 0.999  32.08
->>>>  1.04 Term +   3231   3350  120  2  0  115   48   202 0.980  18.31
->>>>  1.05 PlyA +   3722   3727    6                              -5.80
->>>> 
->>>>  2.00 Prom +   6469   6508   40                              -7.92
->>>>  2.01 Init +   8153   8263  111  1  0   94   83   212 0.998  21.33
->>>>  2.02 Intr +   8531   8709  179  1  2  104   66   408 0.997  40.12
->>>>  2.03 Intr +   8863   9022  160  1  1   89   94   302 0.999  32.08
->>>>  2.04 Term +   9720   9839  120  2  0  115   48   202 0.961  18.31
->>>> 
->>>> Predicted peptide sequence(s):
->>>> 
->>>> Predicted coding sequence(s):
->>>> 
->>>> 
->>>> >HUMRASH|GENSCAN_predicted_peptide_1|189_aa
->>>> MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
->>>> QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
->>>> AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
->>>> CMSCKCVLS
->>>> 
->>>> >HUMRASH|GENSCAN_predicted_CDS_1|570_bp
->>>> atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgacc
->>>> atccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctac
->>>> cggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggc
->>>> caggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt
->>>> gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatc
->>>> aaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctg
->>>> gctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccc
->>>> tacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg
->>>> cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggc
->>>> tgcatgagctgcaagtgtgtgctctcctga
->>>> 
->>>> >HUMRASH|GENSCAN_predicted_peptide_2|189_aa
->>>> MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
->>>> QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
->>>> AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
->>>> CMSCKCVLS
->>>> 
->>>> >HUMRASH|GENSCAN_predicted_CDS_2|570_bp
->>>> atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgacc
->>>> atccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctac
->>>> cggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggc
->>>> caggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt
->>>> gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatc
->>>> aaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctg
->>>> gctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccc
->>>> tacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg
->>>> cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggc
->>>> tgcatgagctgcaagtgtgtgctctcctga
-
-=end