sequence_logo 1.2.3 → 1.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 6b16062d216ed9322e8089cb66d3bb43beb58258
-  data.tar.gz: d7df2af54cb912d5c80c97cc335f1fdde087b9b9
+SHA256:
+  metadata.gz: 32b477a05d970c0504ddd097aba85fae5f2f99da68fcd391fcfae2292742eb6c
+  data.tar.gz: c35413b1a0b77c12ea272a99edfc98a17bae66a3b9b9cee4c5db51995016e070
 SHA512:
-  metadata.gz: 8ce84eb319b246156e83a8134087bb485b0ca01371a690c5793442a57cd9f3d778864e33351cb491b3ed526b07ba9a905a380ba7b79db6d016f43d0b2466b1e2
-  data.tar.gz: e1b0db2b5d9b7e3b4b0373dedc405a024c99474989a42f7e60cf5ab04f2350dbe44091d4d8a9994393fc7b6f0296d502a62b569e103fad8596dea9b531b2958f
+  metadata.gz: 7ca7a02cbecc38cd15b7c622786e0eb0eeb06840133a941ac340cc07f2bc7da0981ea1da4e082e675a7541da2eea2e6cd7d303ca10b8d16327d85884c5a675e4
+  data.tar.gz: 5835d5a6e720753e2555cf0a8dc13a9752f610506bae4c41e1bf582cd75602b8f7940963ffc29b10f1b152e4b5097953c334e8289f5892a3723ddc518d48afb8

data/.gitignore

@@ -3,7 +3,6 @@
 .bundle
 .config
 .yardoc
-Gemfile.lock
 InstalledFiles
 _yardoc
 coverage

data/Gemfile.lock

@@ -0,0 +1,21 @@
+PATH
+  remote: .
+  specs:
+    sequence_logo (1.3.0)
+      bioinform (~> 0.3.1)
+      rmagick (~> 2.13)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    bioinform (0.3.1)
+    rmagick (2.16.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  sequence_logo!
+
+BUNDLED WITH
+   1.16.1

data/lib/sequence_logo/exec/glue_logos.rb

@@ -30,20 +30,19 @@ def make_logo_alignment(aligned_motifs, options)
   alignment
 end
 
-def readlines_from_file_or_stdin(argv, options = {})
+def readlines_from_file_or_stdin(argv, from_stdin: , **options)
   default_options = { source_not_given_msg: 'Specify input data',
                       both_sources_given_msg: 'Specify either file with data or data itself in stdin, not both'}
   options = default_options.merge(options)
-  ## This check fails when glue_logos is run via unicorn. It looks that unicorn daemon redefines isatty of child process
-  # raise options[:both_sources_given_msg]  if !argv.empty? && !$stdin.tty?
-  if !argv.empty?
-    lines = File.readlines(argv.first)
-  elsif !$stdin.tty?
-    lines = $stdin.readlines
+  raise ArgumentError, options[:both_sources_given_msg]  if from_stdin && !argv.empty?
+  raise ArgumentError, options[:source_not_given_msg]  if !from_stdin && argv.empty?
+  if from_stdin || argv == ['-']
+    $stdin.readlines
+  elsif argv.length == 1
+    File.readlines(argv.first)
   else
-    raise ArgumentError, options[:source_not_given_msg]
+    raise ArgumentError, 'alignment should either be in stdin or in file, specified by arglist'
   end
-  lines
 end
 
 def direct_output_filename(output_file)
@@ -65,7 +64,7 @@ begin
   Usage:
     glue_logos <output file> <alignment infos file>
       or
-    <alignment infos file> | glue_logos <output file>
+    <alignment infos file> | glue_logos <output file> --from-stdin
 
   Alignment infos has the following format (tab separated)
   if motif names not specified - filenames are used as labels:
@@ -79,7 +78,7 @@ begin
   total_orientation = :direct
   default_options = { x_unit: 30, y_unit: 60, logo_shift: 300, scheme: 'nucl_simpa',
                       icd_mode: :discrete, threshold_lines: false,
-                      text_size: 24, background_color: 'white' }
+                      text_size: 24, background_color: 'white', from_stdin: false }
   cli = SequenceLogo::CLI.new(default_options)
   cli.instance_eval do
     parser.banner = doc
@@ -102,13 +101,18 @@ begin
         options[:background_fill] = Magick::SolidFill.new(v)
       end
     end
+
+    parser.on('--from-stdin') do 
+      options[:from_stdin] = true
+    end
   end
   options = cli.parse_options!(argv)
 
   output_file = argv.shift
   raise ArgumentError, 'Specify output file'  unless output_file
 
-  alignment_lines = readlines_from_file_or_stdin(argv,  source_not_given_msg: 'Specify alignment infos',
+  alignment_lines = readlines_from_file_or_stdin(argv,  from_stdin: options[:from_stdin],
+                                                        source_not_given_msg: 'Specify alignment infos',
                                                         both_sources_given_msg: 'You can specify alignment infos either from file or from stdin. Don\'t use both sources simultaneously')
   alignment = make_logo_alignment(load_alignment_infos(alignment_lines), options)
 

data/lib/sequence_logo/exec/sequence_logo.rb

@@ -16,9 +16,9 @@ def in_necessary_orientations(objects_to_render, orientation, logo_folder)
   end.flatten
 end
 
-def arglist_augmented_with_stdin(argv)
+def arglist_augmented_with_stdin(argv, from_stdin:)
   result = argv
-  result += $stdin.read.shellsplit  unless $stdin.tty?
+  result += $stdin.read.shellsplit  if from_stdin
   result
 end
 
@@ -35,7 +35,7 @@ begin
   Usage:
     sequence_logo [options] <motif file>...
       or
-    ls pcm_folder/*.pcm | sequence_logo [options]
+    ls pcm_folder/*.pcm | sequence_logo --from-stdin [options]
       or
     sequence_logo --sequence <sequence>...
       or
@@ -47,7 +47,7 @@ begin
   default_options = { x_unit: 30, y_unit: 60, scheme: 'nucl_simpa',
                       orientation: :direct, icd_mode: :discrete, threshold_lines: true,
                       logo_folder: '.', background_color: 'white',
-                      from_dinucleotide: false }
+                      from_dinucleotide: false, from_stdin: false }
   cli = SequenceLogo::CLI.new(default_options)
   cli.instance_eval do
     parser.banner = doc
@@ -73,6 +73,9 @@ begin
         options[:background_fill] = Magick::SolidFill.new(v)
       end
     end
+    parser.on('--from-stdin') {
+      options[:from_stdin] = true
+    }
 
     parser.on('--dinucleotide'){ options[:from_dinucleotide] = true }
   end
@@ -90,7 +93,7 @@ begin
 
   objects_to_render = []
   if options[:sequence]
-    sequences = arglist_augmented_with_stdin(argv)
+    sequences = arglist_augmented_with_stdin(argv, from_stdin: options[:from_stdin])
     raise ArgumentError, 'Specify at least one sequence'  if sequences.empty?
 
     sequences.each do |sequence|
@@ -98,7 +101,7 @@ begin
                             name: File.join(logo_folder, sequence)}
     end
   elsif options[:sequence_w_snp]
-    sequences = arglist_augmented_with_stdin(argv)
+    sequences = arglist_augmented_with_stdin(argv, from_stdin: options[:from_stdin])
     raise ArgumentError, 'Specify at least one sequence'  if sequences.empty?
 
     sequences.each do |sequence_w_snp|
@@ -106,7 +109,7 @@ begin
                             name: File.join(logo_folder, sequence_w_snp.gsub(/[\[\]\/]/, '_'))}
     end
   else
-    filenames = arglist_augmented_with_stdin(argv)
+    filenames = arglist_augmented_with_stdin(argv, from_stdin: options[:from_stdin])
     raise ArgumentError, 'Specify at least one motif file'  if filenames.empty?
 
     filenames.each do |filename|

data/lib/sequence_logo/version.rb

@@ -1,3 +1,3 @@
 module SequenceLogo
-  VERSION = "1.2.3"
+  VERSION = "1.3.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sequence_logo
 version: !ruby/object:Gem::Version
-  version: 1.2.3
+  version: 1.3.0
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-05-14 00:00:00.000000000 Z
+date: 2018-04-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rmagick
@@ -51,6 +51,7 @@ extra_rdoc_files: []
 files:
 - ".gitignore"
 - Gemfile
+- Gemfile.lock
 - LICENSE
 - README.md
 - Rakefile
@@ -118,7 +119,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.5.1
+rubygems_version: 2.7.3
 signing_key: 
 specification_version: 4
 summary: Tool for drawing sequence logos of motifs