iroki 0.0.13 → 0.0.14
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- checksums.yaml +4 -4
- data/.ruby-version +1 -1
- data/.travis.yml +1 -1
- data/README.md +4 -0
- data/iroki.gemspec +1 -1
- data/lib/iroki/biom.rb +12 -1
- data/lib/iroki/color/color.rb +4 -7
- data/lib/iroki/color/single_group_gradient.rb +4 -0
- data/lib/iroki/core_ext/file/file.rb +2 -2
- data/lib/iroki/main/main.rb +1 -1
- data/lib/iroki/version.rb +1 -1
- metadata +4 -4
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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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: 95a7ef76c36216350d0b539cd3e4b259e725e588
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4
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+
data.tar.gz: 9701c392d7bbba6e02bccafe2d12461567a8c5dd
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 8a9a52dd9d3937beb6dabd144ce98599bc67d30a2f0fed0b094f94aa68e7f044f26d3c725db11e941ea497c39319cda26b6c82532fc1c1c5d6fcb41a730c6338
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7
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+
data.tar.gz: d3aed5abfb0cd2b89c06e0e963e47414c7ff082b46d55c467ab5746c85c317b9ff08d97cf682b6e0c75817a72e0f857662ebc7fcbeb660612ac6dce82446578a
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data/.ruby-version
CHANGED
@@ -1 +1 @@
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1
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-
ruby-2.
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1
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+
ruby-2.3.1
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data/.travis.yml
CHANGED
data/README.md
CHANGED
data/iroki.gemspec
CHANGED
@@ -19,7 +19,7 @@ Gem::Specification.new do |spec|
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19
19
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spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
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20
20
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spec.require_paths = ["lib"]
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21
21
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|
22
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-
spec.required_ruby_version = ">= 2.
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22
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+
spec.required_ruby_version = ">= 2.3.1"
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23
23
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24
24
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spec.add_development_dependency "bundler", "~> 1.11"
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25
25
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spec.add_development_dependency "rake", "~> 10.0"
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data/lib/iroki/biom.rb
CHANGED
@@ -23,11 +23,22 @@ module Iroki
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23
23
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def parse
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24
24
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samples = []
|
25
25
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counts = []
|
26
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+
lineno = -1
|
27
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+
first_line_count = -1
|
26
28
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|
27
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-
self.each_line do |line|
|
29
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+
self.each_line.with_index do |line, idx|
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28
30
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unless line.start_with? "#"
|
31
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+
lineno += 1
|
29
32
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sample, *the_counts = line.chomp.split "\t"
|
30
33
|
|
34
|
+
if lineno.zero?
|
35
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+
first_line_count = the_counts.count
|
36
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+
else
|
37
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+
abort_unless first_line_count == the_counts.count,
|
38
|
+
"The biom file has rows with different " +
|
39
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+
"numbers of columns"
|
40
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+
end
|
41
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+
|
31
42
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samples << sample
|
32
43
|
|
33
44
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if the_counts.length == 1
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data/lib/iroki/color/color.rb
CHANGED
@@ -698,7 +698,7 @@ module Iroki
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|
698
698
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WHITE = HSL.from_fraction WHITE_HUE, FULLY_SATURATED, PURE_LIGHT
|
699
699
|
|
700
700
|
DARK_GREEN = RGB.by_hex(COLORS["darkgreen"])
|
701
|
-
GRAY
|
701
|
+
GRAY = RGB.by_hex(COLORS["gray"])
|
702
702
|
|
703
703
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def self.get_tag str, palette=nil
|
704
704
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if str.hex?
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@@ -725,13 +725,10 @@ module Iroki
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725
725
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colors = COLORS
|
726
726
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end
|
727
727
|
|
728
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-
|
729
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-
|
730
|
-
else
|
731
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-
# if passed color other than one defined, return black
|
732
|
-
hex = colors["black"]
|
733
|
-
end
|
728
|
+
abort_unless colors.has_key?(col),
|
729
|
+
"Color '#{col}' is not defined."
|
734
730
|
|
731
|
+
hex = colors[col]
|
735
732
|
%Q{[&!color="#{hex.upcase}"]}
|
736
733
|
end
|
737
734
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end
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@@ -22,6 +22,10 @@ module Iroki
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|
22
22
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attr_accessor :counts, :rel_abunds
|
23
23
|
|
24
24
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def initialize samples, counts, single_color=false
|
25
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+
abort_unless samples.count == counts.count,
|
26
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+
"Samples (#{samples.count}) and counts " +
|
27
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+
"#{counts.count} are different size."
|
28
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+
|
25
29
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@single_color = single_color
|
26
30
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@samples = samples
|
27
31
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@counts = counts
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@@ -55,7 +55,7 @@ module Iroki
|
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55
55
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|
56
56
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|
57
57
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patterns = {}
|
58
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-
Object::File.open(fname).each_line do |line|
|
58
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+
Object::File.open(fname, "rt").each_line do |line|
|
59
59
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unless line.start_with? "#"
|
60
60
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label_tag = ""
|
61
61
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branch_tag = ""
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@@ -131,7 +131,7 @@ module Iroki
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|
131
131
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check_file fname, :name_map
|
132
132
|
|
133
133
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name_map = {}
|
134
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-
Object::File.open(fname).each_line do |line|
|
134
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+
Object::File.open(fname, "rt").each_line do |line|
|
135
135
|
unless line.start_with? "#"
|
136
136
|
oldname, newname = line.chomp.split "\t"
|
137
137
|
|
data/lib/iroki/main/main.rb
CHANGED
@@ -98,7 +98,7 @@ module Iroki
|
|
98
98
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exact_matching: exact,
|
99
99
|
auto_color: auto_color_hash
|
100
100
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else
|
101
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-
samples, counts, is_single_group = Biom.open(biom_f).parse
|
101
|
+
samples, counts, is_single_group = Biom.open(biom_f, "rt").parse
|
102
102
|
|
103
103
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if is_single_group
|
104
104
|
patterns = SingleGroupGradient.new(samples, counts, single_color).patterns
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data/lib/iroki/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: iroki
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
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+
version: 0.0.14
|
5
5
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platform: ruby
|
6
6
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authors:
|
7
7
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- Ryan Moore
|
8
8
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autorequire:
|
9
9
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bindir: exe
|
10
10
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cert_chain: []
|
11
|
-
date: 2016-08-
|
11
|
+
date: 2016-08-04 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundler
|
@@ -222,7 +222,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
222
222
|
requirements:
|
223
223
|
- - ">="
|
224
224
|
- !ruby/object:Gem::Version
|
225
|
-
version: 2.
|
225
|
+
version: 2.3.1
|
226
226
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
227
227
|
requirements:
|
228
228
|
- - ">="
|
@@ -230,7 +230,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
230
230
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version: '0'
|
231
231
|
requirements: []
|
232
232
|
rubyforge_project:
|
233
|
-
rubygems_version: 2.
|
233
|
+
rubygems_version: 2.5.1
|
234
234
|
signing_key:
|
235
235
|
specification_version: 4
|
236
236
|
summary: Command line app and library code for Iroki, a phylogenetic tree customization
|