bio 1.3.1 → 1.4.0

data/sample/demo_genscan_report.rb

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+#
+# = sample/demo_genscan_report.rb - demonstration of Bio::Genscan::Report
+#
+# Copyright::  Copyright (C) 2003 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::Genscan::Report, parser class for Genscan output.
+#
+# == Usage
+#
+# Usage 1: Without arguments, demonstrates using preset sample data.
+#
+#  $ ruby demo_genscan.rb
+#
+# Usage 2: When a "-" is specified as the argument, read data from stdin.
+#
+#  $ cat testdata | ruby demo_genscan.rb -
+#
+# Usage 3: Specify a file containing a Genscan output.
+#
+#  $ ruby demo_genscan.rb file
+#
+# Example usage using test data:
+#
+#  $ ruby -Ilib sample/demo_genscan.rb test/data/genscan/sample.report
+#
+# == Development information
+#
+# The code was moved from lib/bio/appl/genscan/report.rb and modified:
+# * Changed the way to read preset sample data.
+#
+
+require 'bio'
+
+#if __FILE__ == $0
+
+  if ARGV.empty? then
+    report = DATA.read
+  elsif ARGV.size == 1 and ARGV[0] == '-' then
+    ARGV.shift
+    report = $<.read
+  else
+    report = ARGF.read
+  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
+
+### Sample Genscan report is attached below.
+### The lines after the "__END__" can be accessed by using "DATA".
+
+__END__
+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

data/sample/demo_gff1.rb

@@ -0,0 +1,49 @@
+#
+# = sample/demo_gff1.rb - very simple demonstration of Bio::GFF
+#
+# Copyright::  Copyright (C) 2003, 2005
+#              Toshiaki Katayama <k@bioruby.org>
+#              2006  Jan Aerts <jan.aerts@bbsrc.ac.uk>
+#              2008  Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+#
+# == Description
+#
+# Very simple demonstration of Bio::GFF, parser classes for GFF formatted
+# text.
+#
+# == Usage
+#
+# Simply run this script.
+#
+#  $ ruby demo_gff1.rb
+#
+# == To do
+#
+# Bio::GFF and related classes have many functions, and we should write
+# more example and/or demonstration codes.
+#
+# == Development information
+#
+# The code was moved from lib/bio/db/gff.rb.
+#
+
+require 'bio'
+
+#if __FILE__ == $0
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  this_gff =  "SEQ1\tEMBL\tatg\t103\t105\t.\t+\t0\n"
+  this_gff << "SEQ1\tEMBL\texon\t103\t172\t.\t+\t0\n"
+  this_gff << "SEQ1\tEMBL\tsplice5\t172\t173\t.\t+\t.\n"
+  this_gff << "SEQ1\tnetgene\tsplice5\t172\t173\t0.94\t+\t.\n"
+  this_gff << "SEQ1\tgenie\tsp5-20\t163\t182\t2.3\t+\t.\n"
+  this_gff << "SEQ1\tgenie\tsp5-10\t168\t177\t2.1\t+\t.\n"
+  this_gff << "SEQ1\tgrail\tATG\t17\t19\t2.1\t-\t0\n"
+  p Bio::GFF.new(this_gff)
+#end

data/sample/demo_go.rb

@@ -0,0 +1,98 @@
+#
+# = sample/demo_go.rb - demonstration of Bio::GO, classes for Gene Ontology
+#
+# Copyright::   Copyright (C) 2003 
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::GO, classes for Gene Ontology.
+#
+# == Requirement
+#
+# Internet connection is needed.
+#
+# == Usage
+#
+# Simply run this script.
+#
+#  $ ruby demo_go.rb
+#
+# == Note
+#
+# The code was originally written in 2003, and it can only parse GO format
+# that is deprecated and no new data is available after August 2009.
+#
+# == Development information
+#
+# The code was moved from lib/bio/db/go.rb.
+#
+
+require 'bio'
+
+#if __FILE__ == $0
+
+  def wget(url)
+    Bio::Command.read_uri(url)
+  end
+
+
+
+  go_c_url = 'http://www.geneontology.org/ontology/component.ontology'
+  ga_url = 'http://www.geneontology.org/gene-associations/gene_association.sgd.gz'
+  e2g_url = 'http://www.geneontology.org/external2go/spkw2go'
+
+
+
+  puts "\n #==> Bio::GO::Ontology"
+  p go_c_url
+  component_ontology = wget(go_c_url)
+  comp = Bio::GO::Ontology.new(component_ontology)
+
+  [['0003673', '0005632'],
+    ['0003673', '0005619'],
+    ['0003673', '0004649']].each {|pair|
+    puts
+    p pair
+    p [:pair, pair.map {|i| [comp.id2term[i], comp.goid2term(i)] }]
+    puts "\n #==> comp.bfs_shortest_path(pair[0], pair[1])"
+    p comp.bfs_shortest_path(pair[0], pair[1])
+  }
+
+
+  puts "\n #==> Bio::GO::External2go"
+  p e2g_url
+  spkw2go = Bio::GO::External2go.parser(wget(e2g_url))
+
+  puts "\n #==> spkw2go.dbs"
+  p spkw2go.dbs
+
+  puts "\n #==> spkw2go[1]"
+  p spkw2go[1]
+
+
+
+  require 'zlib'
+  puts "\n #==> Bio::GO::GeenAssociation"
+  p ga_url
+  #
+  # The workaround (Zlib::MAX_WBITS + 32) is taken from:
+  #  http://d.hatena.ne.jp/ksef-3go/20070924/1190563143
+  #
+  ga = Zlib::Inflate.new(Zlib::MAX_WBITS + 32).inflate(wget(ga_url))
+  #ga = Zlib::Inflate.inflate(wget(ga_url))
+  ga = Bio::GO::GeneAssociation.parser(ga)
+
+  puts "\n #==> ga.size"
+  p ga.size
+
+  puts "\n #==> ga[100]"
+  p ga[100]
+
+
+
+
+  
+#end

data/sample/demo_hmmer_report.rb

@@ -0,0 +1,149 @@
+#
+# = sample/demo_hmmer_report.rb - demonstration of Bio::HMMER::Report
+#
+# Copyright::   Copyright (C) 2002 
+#               Hiroshi Suga <suga@biophys.kyoto-u.ac.jp>,
+# Copyright::   Copyright (C) 2005 
+#               Masashi Fujita <fujita@kuicr.kyoto-u.ac.jp>
+# License::     The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::HMMER::Report (HMMER output parser).
+#
+# Note that it (and Bio::HMMER::Report) supports HMMER 2.x.
+# HMMER 3.x is currently not supported.
+#
+# == Usage
+#
+# Specify a file containing a HMMER result.
+#
+#  $ ruby demo_hmmer_report.rb file
+#
+# Example usage using test data:
+#
+#  $ ruby -Ilib sample/demo_hmmer_report.rb test/data/HMMER/hmmsearch.out
+#  $ ruby -Ilib sample/demo_blast_report.rb test/data/HMMER/hmmpfam.out
+#
+# == Development information
+#
+# The code was moved from lib/bio/appl/hmmer/report.rb.
+#
+
+require 'bio'
+
+#if __FILE__ == $0
+
+=begin
+
+  #
+  # for multiple reports in a single output file (hmmpfam)
+  #
+  Bio::HMMER.reports(ARGF.read) do |report|
+    report.hits.each do |hit|
+      hit.hsps.each do |hsp|
+      end
+    end
+  end
+
+=end
+
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  rep = Bio::HMMER::Report.new(ARGF.read)
+  p rep
+
+  indent = 18
+
+  puts "### hmmer result"
+  print "name : ".rjust(indent)
+  p  rep.program['name']
+  print "version : ".rjust(indent)
+  p rep.program['version']
+  print "copyright : ".rjust(indent)
+  p rep.program['copyright']
+  print "license : ".rjust(indent)
+  p rep.program['license']
+
+  print "HMM file : ".rjust(indent)
+  p rep.parameter['HMM file']
+  print "Sequence file : ".rjust(indent)
+  p rep.parameter['Sequence file']
+
+  print "Query sequence : ".rjust(indent)
+  p rep.query_info['Query sequence']
+  print "Accession : ".rjust(indent)
+  p rep.query_info['Accession']
+  print "Description : ".rjust(indent)
+  p rep.query_info['Description']
+
+  rep.each do |hit|
+    puts "## each hit"
+    print "accession : ".rjust(indent)
+    p [ hit.accession, hit.target_id, hit.hit_id, hit.entry_id ]
+    print "description : ".rjust(indent)
+    p [ hit.description, hit.definition ]
+    print "target_def : ".rjust(indent)
+    p hit.target_def
+    print "score : ".rjust(indent)
+    p [ hit.score, hit.bit_score ]
+    print "evalue : ".rjust(indent)
+    p hit.evalue
+    print "num : ".rjust(indent)
+    p hit.num
+
+    hit.each do |hsp|
+      puts "## each hsp"
+      print "accession : ".rjust(indent)
+      p [ hsp.accession, hsp.target_id ]
+      print "domain : ".rjust(indent)
+      p hsp.domain
+      print "seq_f : ".rjust(indent)
+      p hsp.seq_f
+      print "seq_t : ".rjust(indent)
+      p hsp.seq_t
+      print "seq_ft : ".rjust(indent)
+      p hsp.seq_ft
+      print "hmm_f : ".rjust(indent)
+      p hsp.hmm_f
+      print "hmm_t : ".rjust(indent)
+      p hsp.hmm_t
+      print "hmm_ft : ".rjust(indent)
+      p hsp.hmm_ft
+      print "score : ".rjust(indent)
+      p [ hsp.score, hsp.bit_score ]
+      print "evalue : ".rjust(indent)
+      p hsp.evalue
+      print "midline : ".rjust(indent)
+      p hsp.midline
+      print "hmmseq : ".rjust(indent)
+      p hsp.hmmseq
+      print "flatseq : ".rjust(indent)
+      p hsp.flatseq
+      print "query_frame : ".rjust(indent)
+      p hsp.query_frame
+      print "target_frame : ".rjust(indent)
+      p hsp.target_frame
+
+      print "query_seq : ".rjust(indent)
+      p hsp.query_seq		# hmmseq, flatseq
+      print "target_seq : ".rjust(indent)
+      p hsp.target_seq		# flatseq, hmmseq
+      print "target_from : ".rjust(indent)
+      p hsp.target_from		# seq_f, hmm_f
+      print "target_to : ".rjust(indent)
+      p hsp.target_to		# seq_t, hmm_t
+      print "query_from : ".rjust(indent)
+      p hsp.query_from		# hmm_f, seq_f
+      print "query_to : ".rjust(indent)
+      p hsp.query_to		# hmm_t, seq_t
+    end 
+  end
+
+#end 
+