sequence_logo 1.3.4 → 1.3.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/sequence_logo/exec/sequence_logo.rb +10 -0
- data/lib/sequence_logo/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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SHA256:
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3
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metadata.gz:
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4
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data.tar.gz:
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3
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metadata.gz: c619eecefa46220873c431f87a9c8d20a9a8d8d26093c213df04c366d19c0434
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4
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data.tar.gz: a587739504949d122f6cf13691db350bf566bd9089c45b3c59035e6c78aa16e3
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SHA512:
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metadata.gz:
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7
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data.tar.gz:
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metadata.gz: a8b8cfe480444b5aa07e07577ba4911827fcb36ddbb18c1b6e55c27fb0ea2aad796ccdd6c7bf5df810389850b342ed539d5751dcad3fe6592b86b0a672e435c8
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7
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data.tar.gz: ff374cc30952e3c124b8ac8b2673e2f64ed1a15f4b31a37bc9eaae26e7ececaf330c7dac27b62b1780568675b6b89ee4def1636be27c382b1ca568a839510ba6
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@@ -82,6 +82,8 @@ begin
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}
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parser.on('--dinucleotide'){ options[:from_dinucleotide] = true }
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parser.on('--ppm-count N', 'Multiply PPM by N to get PCM'){|value| options[:ppm_count] = Float(value) }
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end
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options = cli.parse_options!(argv)
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@@ -123,6 +125,14 @@ begin
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ppm = Bioinform::MotifModel::PCM.from_file(filename, validator: Bioinform::MotifModel::PCM::DIFFERENT_COUNTS_VALIDATOR)
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end
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if options[:ppm_count]
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new_matrix = ppm.matrix.map{|position|
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sum = position.sum(0.0)
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position.map{|el| el * options[:ppm_count] / sum}
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}
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ppm = Bioinform::MotifModel::PCM.new(new_matrix)
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end
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logo = SequenceLogo::PPMLogo.new( ppm,
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icd_mode: options[:icd_mode],
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enable_threshold_lines: options[:threshold_lines])
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