sequence_logo 1.0.4 → 1.0.5
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/glue_logos.rb +11 -8
- data/lib/sequence_logo/version.rb +1 -1
- metadata +7 -7
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA1:
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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: 4a3490689a2063bc701ce8f9e50d270dfa22ba7f
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4
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data.tar.gz: 9ea7a0c46fdbeeb7d5a21ecd29b6959079ad19b5
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5
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SHA512:
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-
metadata.gz:
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data.tar.gz:
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6
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metadata.gz: 57241901c85514889fb98f22ac717a480e36f5ab5917217797532e6d647f9364f3353316bf632c30574411c666d55515d0ac12ca08f7f23bd713149a7ad99116
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7
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data.tar.gz: ca2a674b8f2fa4db523f09a7f468a57f499ff8ab0edeb8d532b20dfa3fd0234b3341925ff53c5509b5fecc1780b6bbfed74db9d57721f0328f149ebdb13206cb
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@@ -6,13 +6,14 @@ def generate_glued_logo(alignment_infos, options, total_orientation, output_file
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logos = {}
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logo_filenames = []
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rightmost_side = alignment_infos.map do |line|
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9
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-
filename, shift, orientation = line.strip.split("\t")
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9
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filename, shift, orientation, motif_name = line.strip.split("\t")
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shift = shift.to_i
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shift + get_ppm_from_file(filename).length
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end.max
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alignment_infos.each do |line|
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filename, shift, orientation = line.strip.split("\t")
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15
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filename, shift, orientation, motif_name = line.strip.split("\t")
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motif_name ||= CGI.unescape(File.basename(filename, File.extname(filename)))
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ppm = get_ppm_from_file(filename)
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shift = shift.to_i
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raise 'Unknown orientation' unless %w[direct revcomp].include?(orientation.downcase)
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@@ -29,9 +30,9 @@ def generate_glued_logo(alignment_infos, options, total_orientation, output_file
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when 'revcomp'
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SequenceLogo.draw_logo(ppm.revcomp, options).write(logo_filename)
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else
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raise "Unknown orientation #{orientation} for #{
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raise "Unknown orientation #{orientation} for #{motif_name}"
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end
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-
logos[logo_filename] = {shift: shift, length: ppm.length, name:
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logos[logo_filename] = {shift: shift, length: ppm.length, name: motif_name}
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end
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SequenceLogo.glue_files(logos, output_file, options)
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@@ -45,10 +46,12 @@ begin
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or
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<alignment infos file> | glue_logos <output file>
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Alignment infos has format
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-
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Alignment infos has the following format (tab separated)
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if motif names not specified - filenames are used as labels:
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pcm_file_1 shift_1 orientation_1 [motif_name_1]
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pcm_file_2 shift_2 orientation_2 [motif_name_2]
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pcm_file_3 shift_3 orientation_3 [motif_name_3]
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+
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EOS
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argv = ARGV
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metadata
CHANGED
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@@ -1,27 +1,27 @@
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--- !ruby/object:Gem::Specification
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name: sequence_logo
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version: !ruby/object:Gem::Version
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version: 1.0.
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version: 1.0.5
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platform: ruby
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authors:
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- Ilya Vorontsov
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-
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date: 2014-02-20 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rmagick
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requirement: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: 2.13.1
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: 2.13.1
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description: |
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@@ -35,7 +35,7 @@ executables:
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extensions: []
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extra_rdoc_files: []
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files:
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-
- .gitignore
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- ".gitignore"
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- Gemfile
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- LICENSE
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- README.md
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@@ -80,12 +80,12 @@ require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
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-
- -
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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-
- -
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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