sequence_logo 1.0.4 → 1.0.5

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Files changed (4) hide show
  1. checksums.yaml +4 -4
  2. data/lib/sequence_logo/exec/glue_logos.rb +11 -8
  3. data/lib/sequence_logo/version.rb +1 -1
  4. metadata +7 -7
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  SHA1:
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- metadata.gz: 0c7bf6142b7da024066e931674fe7a2d95329725
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- data.tar.gz: 43a219e7e1816925b0e6a35ce46373157b06be34
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+ metadata.gz: 4a3490689a2063bc701ce8f9e50d270dfa22ba7f
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+ data.tar.gz: 9ea7a0c46fdbeeb7d5a21ecd29b6959079ad19b5
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  SHA512:
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- metadata.gz: 93cb221175a8a7769f272ed0cdfca146ed838dbb4851a6717f06d73101e1cf9be5473f8e6a26dab53ac8ab61f44330ccd54b6e6b0191cf8b064ef7d46d942617
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- data.tar.gz: 5e979afbf8c4b1e6d47e49955318c38e8416e585e129440d9b8c313d94b1885233ec5233fcc37c702e236904cfc92a18e5739286565b1dd0e8862b3c6bac65f0
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+ metadata.gz: 57241901c85514889fb98f22ac717a480e36f5ab5917217797532e6d647f9364f3353316bf632c30574411c666d55515d0ac12ca08f7f23bd713149a7ad99116
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+ data.tar.gz: ca2a674b8f2fa4db523f09a7f468a57f499ff8ab0edeb8d532b20dfa3fd0234b3341925ff53c5509b5fecc1780b6bbfed74db9d57721f0328f149ebdb13206cb
data/lib/sequence_logo/exec/glue_logos.rb CHANGED
@@ -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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- filename, shift, orientation = line.strip.split("\t")
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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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+ 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)
@@ -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 #{filename}"
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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: CGI.unescape(File.basename(filename, File.extname(filename)))}
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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)
@@ -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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- pcm_file_1 shift_1 orientation_1
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- pcm_file_2 shift_2 orientation_2
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- pcm_file_3 shift_3 orientation_3
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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
data/lib/sequence_logo/version.rb CHANGED
@@ -1,3 +1,3 @@
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  module SequenceLogo
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- VERSION = "1.0.4"
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+ VERSION = "1.0.5"
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  end
metadata CHANGED
@@ -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: 1.0.4
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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: 2014-01-14 00:00:00.000000000 Z
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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: |
@@ -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
@@ -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: []