lib/bio/appl/genscan/report.rb in bio-1.3.1 vs lib/bio/appl/genscan/report.rb in bio-1.4.0
- old
+ new
@@ -372,181 +372,5 @@
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