bio 1.3.1 → 1.4.0

data/lib/bio.rb

@@ -113,8 +113,9 @@ module Bio
   ## other formats
 
   autoload :FastaFormat,    'bio/db/fasta'
-  autoload :FastaNumericFormat, 'bio/db/fasta' # change to FastaFormat::Numeric ?
-  autoload :FastaDefline,       'bio/db/fasta' # change to FastaFormat::Defline
+  autoload :FastaNumericFormat, 'bio/db/fasta/qual' # change to FastaFormat::Numeric ?
+  autoload :FastaDefline,       'bio/db/fasta/defline' # change to FastaFormat::Defline ?
+  autoload :Fastq,          'bio/db/fastq'
   autoload :GFF,            'bio/db/gff'
   autoload :AAindex,        'bio/db/aaindex'
   autoload :AAindex1,       'bio/db/aaindex' # change to AAindex::AAindex1 ?
@@ -130,10 +131,22 @@ module Bio
   autoload :REBASE,         'bio/db/rebase'
   autoload :SOFT,           'bio/db/soft'
   autoload :Lasergene,      'bio/db/lasergene'
+  autoload :SangerChromatogram, 'bio/db/sanger_chromatogram/chromatogram'
+  autoload :Scf,                'bio/db/sanger_chromatogram/scf'
+  autoload :Abif,               'bio/db/sanger_chromatogram/abif'
 
   autoload :Newick,         'bio/db/newick'
   autoload :Nexus,          'bio/db/nexus'
 
+  autoload :PhyloXML,       'bio/db/phyloxml/phyloxml_elements'
+  # Bio::Taxonomy will be moved to other file
+  autoload :Taxonomy,       'bio/db/phyloxml/phyloxml_elements'
+  ## below are described in bio/db/phyloxml/phyloxml_elements.rb
+  #module PhyloXML
+  #  autoload :Parser,       'bio/db/phyloxml/phyloxml_parser'
+  #  autoload :Writer,       'bio/db/phyloxml/phyloxml_writer'
+  #end
+
   ### IO interface modules
 
   autoload :Registry,       'bio/io/registry'
@@ -179,10 +192,12 @@ module Bio
     autoload :SOAP,         'bio/io/ebisoap'
   end
 
-  class NCBI
-    autoload :SOAP,       'bio/io/ncbisoap'
-    autoload :REST,       'bio/io/ncbirest'
-  end
+  autoload :NCBI,         'bio/io/ncbirest'
+  ## below are described in bio/io/ncbirest.rb
+  #class NCBI
+  #  autoload :SOAP,       'bio/io/ncbisoap'
+  #  autoload :REST,       'bio/io/ncbirest'
+  #end
 
   autoload :TogoWS,       'bio/io/togows'
 

data/lib/bio/appl/bl2seq/report.rb

@@ -1,12 +1,12 @@
 #
 # = bio/appl/bl2seq/report.rb - bl2seq (BLAST 2 sequences) parser
 # 
-# Copyright:: Copyright (C) 2005 GOTO Naohisa <ng@bioruby.org>
+# Copyright:: Copyright (C) 2005 Naohisa Goto <ng@bioruby.org>
 # License::   The Ruby License
 #
-#  $Id: report.rb,v 1.8 2007/04/05 23:35:39 trevor Exp $
+#  $Id:$
 #
-# Bio::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.
+# Bio::Blast::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.
 #
 # = Acknowledgements
 #
@@ -22,15 +22,16 @@ class Blast
 
   class Bl2seq
 
-    # Bio::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.
+    # Bio::Blast::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.
     # It inherits Bio::Blast::Default::Report.
     # Most of its methods are the same as Bio::Blast::Default::Report,
     # but it lacks many methods.
     class Report < Bio::Blast::Default::Report
 
       # Delimiter of each entry. Bio::FlatFile uses it.
-      # In Bio::Bl2seq::Report, it it nil (1 entry 1 file).
+      # In Bio::Blast::Bl2seq::Report, it it nil (1 entry 1 file).
       DELIMITER = RS = nil
+      DELIMITER_OVERRUN = nil
 
       undef format0_parse_header
       undef program, version, version_number, version_date,
@@ -77,9 +78,9 @@ class Blast
         end
       end #class F0dbstat
 
-      # Bio::Bl2seq::Report::Iteration stores information about
+      # Bio::Blast::Bl2seq::Report::Iteration stores information about
       # a iteration.
-      # Normally, it may contain some Bio::Bl2seq::Report::Hit objects.
+      # Normally, it may contain some Bio::Blast::Bl2seq::Report::Hit objects.
       #
       # Note that its main existance reason is to keep complatibility
       # between Bio::Blast::Default::Report::* classes.
@@ -99,7 +100,7 @@ class Blast
         end
 
         # Returns the hits of the iteration.
-        # It returns an array of Bio::Bl2seq::Report::Hit objects.
+        # It returns an array of Bio::Blast::Bl2seq::Report::Hit objects.
         def hits; @hits; end
 
         undef message, pattern_in_database, 
@@ -108,14 +109,14 @@ class Blast
           converged?
       end #class Iteration
 
-      # Bio::Bl2seq::Report::Hit contains information about a hit.
+      # Bio::Blast::Bl2seq::Report::Hit contains information about a hit.
       # It may contain some Bio::Blast::Default::Report::HSP objects.
       # All methods are the same as Bio::Blast::Default::Report::Hit class.
       # Please refer to Bio::Blast::Default::Report::Hit.
       class Hit < Bio::Blast::Default::Report::Hit
       end #class Hit
 
-      # Bio::Bl2seq::Report::HSP holds information about the hsp
+      # Bio::Blast::Bl2seq::Report::HSP holds information about the hsp
       # (high-scoring segment pair).
       # NOTE that the HSP class below is NOT used because
       # Ruby's constants namespace are normally statically determined
@@ -132,198 +133,6 @@ end #module Bio
 
 ######################################################################
 
-if __FILE__ == $0
-
-  Bio::FlatFile.open(Bio::Blast::Bl2seq::Report, ARGF) do |ff|
-  ff.each do |rep|
-
-  print "# === Bio::Blast::Bl2seq::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 "  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 "# === Iterations\n"
-  puts
-  print "  rep.itrerations.each do |itr|\n"
-  puts
-
-  rep.iterations.each do |itr|
-      
-  print "# --- Bio::Blast::Bl2seq::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_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::Bl2seq::Default::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?
-
-  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::Default::Report::HSP (Bio::Blast::Bl2seq::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
-
-  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
-
-######################################################################
-
 =begin
 
 = Bio::Blast::Bl2seq::Report

data/lib/bio/appl/blast/format0.rb

@@ -1248,196 +1248,3 @@ module Bio
   end #class Blast
 end #module Bio
 
-######################################################################
-
-if __FILE__ == $0
-
-  Bio::FlatFile.open(Bio::Blast::Default::Report, ARGF) do |ff|
-  ff.each do |rep|
-
-  print "# === Bio::Blast::Default::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 "  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 "# === Iterations\n"
-  puts
-  print "  rep.itrerations.each do |itr|\n"
-  puts
-
-  rep.iterations.each do |itr|
-      
-  print "# --- Bio::Blast::Default::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_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::Default::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?
-
-  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::Default::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
-
-  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
-
-######################################################################