wrnap 0.7.0 → 0.9.0
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- checksums.yaml +4 -4
- data/lib/wrnap/global/rna.rb +10 -0
- data/lib/wrnap/global/rna/context.rb +6 -2
- data/lib/wrnap/global/rna/extensions.rb +16 -0
- data/lib/wrnap/version.rb +1 -1
- metadata +3 -12
- data/.idea/.name +0 -1
- data/.idea/.rakeTasks +0 -7
- data/.idea/encodings.xml +0 -5
- data/.idea/misc.xml +0 -5
- data/.idea/modules.xml +0 -9
- data/.idea/scopes/scope_settings.xml +0 -5
- data/.idea/vcs.xml +0 -7
- data/.idea/workspace.xml +0 -169
- data/.idea/wrnap.iml +0 -49
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA1:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: ac1239c0ba7934c50ad98b76df47db8e55fece20
|
|
4
|
+
data.tar.gz: 968842380493afb6092cce95df09d3c4d61bb3c4
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: d3ca46aa20984438b365a325d6a63d0b90f68d8bbd9e238cdfb2927685fe11360a696a9d78dc18d75118ba3a47a1a9e3de0524f0ebf19ec2854aa3620fc2f9cc
|
|
7
|
+
data.tar.gz: 0620bed745bc6bed2a2615792422bce97ce31b77e6ad12761dfec85716c8f3577a4c8f7ab7d70934e0cd7c4e49afc1ef8c06fc30a8b8eb9188a11a3582b08168
|
data/lib/wrnap/global/rna.rb
CHANGED
|
@@ -102,6 +102,12 @@ module Wrnap
|
|
|
102
102
|
|
|
103
103
|
alias :empty_str :empty_structure
|
|
104
104
|
|
|
105
|
+
def no_structure
|
|
106
|
+
self.class.init_from_string(seq, nil, nil, name)
|
|
107
|
+
end
|
|
108
|
+
|
|
109
|
+
alias :no_str :no_structure
|
|
110
|
+
|
|
105
111
|
def one_structure(structure_1)
|
|
106
112
|
self.class.init_from_string(seq, structure_1.is_a?(Symbol) ? send(structure_1) : structure_1, nil, name)
|
|
107
113
|
end
|
|
@@ -137,6 +143,10 @@ module Wrnap
|
|
|
137
143
|
Wrnap::Package.lookup(package_name).run(self, options)
|
|
138
144
|
end
|
|
139
145
|
|
|
146
|
+
def ==(other_rna)
|
|
147
|
+
other_rna.kind_of?(Wrnap::Global::Rna) ? [seq, str_1, str_2] == [other_rna.seq, other_rna.str_1, other_rna.str_2] : super
|
|
148
|
+
end
|
|
149
|
+
|
|
140
150
|
def method_missing(name, *args, &block)
|
|
141
151
|
if (name_str = "#{name}") =~ /^run_\w+$/
|
|
142
152
|
run(name_str.gsub(/^run_/, ""), *args)
|
|
@@ -40,7 +40,7 @@ module Wrnap
|
|
|
40
40
|
sequence: self.sequence,
|
|
41
41
|
structure: options[:rna][:structure] || options[:rna][:str_1] || options[:rna][:str],
|
|
42
42
|
second_structure: options[:rna][:second_structure] || options[:rna][:str_2],
|
|
43
|
-
comment: options[:rna][:comment] || options[:rna][:name]
|
|
43
|
+
comment: options[:rna][:comment] || options[:rna][:name] || identifier
|
|
44
44
|
})
|
|
45
45
|
|
|
46
46
|
remove_instance_variable(:@sequence)
|
|
@@ -125,8 +125,12 @@ module Wrnap
|
|
|
125
125
|
end
|
|
126
126
|
end
|
|
127
127
|
|
|
128
|
+
def identifier
|
|
129
|
+
"%s %d %s %d" % [accession, from, plus_strand? ? ?+ : ?-, to]
|
|
130
|
+
end
|
|
131
|
+
|
|
128
132
|
def inspect
|
|
129
|
-
super.gsub(/((\w(::)?)+)>$/) { |_| "%s %
|
|
133
|
+
super.gsub(/((\w(::)?)+)>$/) { |_| "%s %s>" % [identifier, $1] }
|
|
130
134
|
end
|
|
131
135
|
end
|
|
132
136
|
end
|
|
@@ -33,6 +33,10 @@ module Wrnap
|
|
|
33
33
|
def shuffle(sequence, token_length = 2)
|
|
34
34
|
Shuffle.new(sequence).shuffle(token_length)
|
|
35
35
|
end
|
|
36
|
+
|
|
37
|
+
def structure_from_bp_list(length, base_pairs)
|
|
38
|
+
base_pairs.to_a.map(&:to_a).map(&:sort).inject("." * length) { |structure, (i, j)| structure.tap { structure[i] = ?(; structure[j] = ?) } }
|
|
39
|
+
end
|
|
36
40
|
end
|
|
37
41
|
|
|
38
42
|
module InstanceMethods
|
|
@@ -50,6 +54,18 @@ module Wrnap
|
|
|
50
54
|
end
|
|
51
55
|
|
|
52
56
|
module OneStructureBasedMethods
|
|
57
|
+
def helices(structure)
|
|
58
|
+
array = base_pairs(structure).sort_by(&:first).map(&:to_a)
|
|
59
|
+
|
|
60
|
+
unless array.empty?
|
|
61
|
+
array[1..-1].inject([[array.first]]) do |bins, (i, j)|
|
|
62
|
+
bins.tap { bins[-1][-1] == [i - 1, j + 1] ? bins[-1] << [i, j] : bins << [[i, j]] }
|
|
63
|
+
end
|
|
64
|
+
else
|
|
65
|
+
[]
|
|
66
|
+
end
|
|
67
|
+
end
|
|
68
|
+
|
|
53
69
|
def max_bp_distance(structure)
|
|
54
70
|
base_pairs(structure).count + ((structure.length - 3) / 2.0).floor
|
|
55
71
|
end
|
data/lib/wrnap/version.rb
CHANGED
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: wrnap
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.
|
|
4
|
+
version: 0.9.0
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Evan Senter
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2014-
|
|
11
|
+
date: 2014-07-03 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: bundler
|
|
@@ -130,15 +130,6 @@ extensions: []
|
|
|
130
130
|
extra_rdoc_files: []
|
|
131
131
|
files:
|
|
132
132
|
- ".gitignore"
|
|
133
|
-
- ".idea/.name"
|
|
134
|
-
- ".idea/.rakeTasks"
|
|
135
|
-
- ".idea/encodings.xml"
|
|
136
|
-
- ".idea/misc.xml"
|
|
137
|
-
- ".idea/modules.xml"
|
|
138
|
-
- ".idea/scopes/scope_settings.xml"
|
|
139
|
-
- ".idea/vcs.xml"
|
|
140
|
-
- ".idea/workspace.xml"
|
|
141
|
-
- ".idea/wrnap.iml"
|
|
142
133
|
- Gemfile
|
|
143
134
|
- LICENSE.md
|
|
144
135
|
- README.md
|
|
@@ -197,7 +188,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
197
188
|
version: '0'
|
|
198
189
|
requirements: []
|
|
199
190
|
rubyforge_project:
|
|
200
|
-
rubygems_version: 2.
|
|
191
|
+
rubygems_version: 2.3.0
|
|
201
192
|
signing_key:
|
|
202
193
|
specification_version: 4
|
|
203
194
|
summary: A comprehensive wrapper (wRNApper) for various RNA CLI programs.
|
data/.idea/.name
DELETED
|
@@ -1 +0,0 @@
|
|
|
1
|
-
wrnap
|
data/.idea/.rakeTasks
DELETED
|
@@ -1,7 +0,0 @@
|
|
|
1
|
-
<?xml version="1.0" encoding="UTF-8"?>
|
|
2
|
-
<Settings><!--This file was automatically generated by Ruby plugin.
|
|
3
|
-
You are allowed to:
|
|
4
|
-
1. Remove rake task
|
|
5
|
-
2. Add existing rake tasks
|
|
6
|
-
To add existing rake tasks automatically delete this file and reload the project.
|
|
7
|
-
--><RakeGroup description="" fullCmd="" taksId="rake"><RakeTask description="Build wrnap-0.5.1.gem into the pkg directory" fullCmd="build" taksId="build" /><RakeTask description="Build and install wrnap-0.5.1.gem into system gems" fullCmd="install" taksId="install" /><RakeTask description="Create tag v0.5.1 and build and push wrnap-0.5.1.gem to Rubygems" fullCmd="release" taksId="release" /></RakeGroup></Settings>
|
data/.idea/encodings.xml
DELETED
data/.idea/misc.xml
DELETED
data/.idea/modules.xml
DELETED
data/.idea/vcs.xml
DELETED
data/.idea/workspace.xml
DELETED
|
@@ -1,169 +0,0 @@
|
|
|
1
|
-
<?xml version="1.0" encoding="UTF-8"?>
|
|
2
|
-
<project version="4">
|
|
3
|
-
<component name="ChangeListManager">
|
|
4
|
-
<list default="true" id="f215766d-a45c-47cc-a7d7-9487868cd8b4" name="Default" comment="">
|
|
5
|
-
<change type="MODIFICATION" beforePath="$PROJECT_DIR$/lib/wrnap/package/base.rb" afterPath="$PROJECT_DIR$/lib/wrnap/package/base.rb" />
|
|
6
|
-
</list>
|
|
7
|
-
<ignored path="wrnap.iws" />
|
|
8
|
-
<ignored path=".idea/workspace.xml" />
|
|
9
|
-
<option name="TRACKING_ENABLED" value="true" />
|
|
10
|
-
<option name="SHOW_DIALOG" value="false" />
|
|
11
|
-
<option name="HIGHLIGHT_CONFLICTS" value="true" />
|
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12
|
-
<option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
|
|
13
|
-
<option name="LAST_RESOLUTION" value="IGNORE" />
|
|
14
|
-
</component>
|
|
15
|
-
<component name="ChangesViewManager" flattened_view="true" show_ignored="false" />
|
|
16
|
-
<component name="CreatePatchCommitExecutor">
|
|
17
|
-
<option name="PATCH_PATH" value="" />
|
|
18
|
-
</component>
|
|
19
|
-
<component name="DaemonCodeAnalyzer">
|
|
20
|
-
<disable_hints />
|
|
21
|
-
</component>
|
|
22
|
-
<component name="FavoritesManager">
|
|
23
|
-
<favorites_list name="wrnap" />
|
|
24
|
-
</component>
|
|
25
|
-
<component name="FileEditorManager">
|
|
26
|
-
<leaf>
|
|
27
|
-
<file leaf-file-name="wrnap.rb" pinned="false" current="true" current-in-tab="true">
|
|
28
|
-
<entry file="file://$PROJECT_DIR$/lib/wrnap.rb">
|
|
29
|
-
<provider selected="true" editor-type-id="text-editor">
|
|
30
|
-
<state vertical-scroll-proportion="-0.074179746" vertical-offset="52" max-vertical-offset="1183">
|
|
31
|
-
<caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
|
|
32
|
-
<folding />
|
|
33
|
-
</state>
|
|
34
|
-
</provider>
|
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-
</entry>
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-
</file>
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|
-
</leaf>
|
|
38
|
-
</component>
|
|
39
|
-
<component name="FindManager">
|
|
40
|
-
<FindUsagesManager>
|
|
41
|
-
<setting name="OPEN_NEW_TAB" value="true" />
|
|
42
|
-
</FindUsagesManager>
|
|
43
|
-
</component>
|
|
44
|
-
<component name="Git.Settings">
|
|
45
|
-
<option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
|
|
46
|
-
</component>
|
|
47
|
-
<component name="ProjectFrameBounds">
|
|
48
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-
<option name="y" value="22" />
|
|
49
|
-
<option name="width" value="1280" />
|
|
50
|
-
<option name="height" value="774" />
|
|
51
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-
</component>
|
|
52
|
-
<component name="ProjectLevelVcsManager" settingsEditedManually="false">
|
|
53
|
-
<OptionsSetting value="true" id="Add" />
|
|
54
|
-
<OptionsSetting value="true" id="Remove" />
|
|
55
|
-
<OptionsSetting value="true" id="Checkout" />
|
|
56
|
-
<OptionsSetting value="true" id="Update" />
|
|
57
|
-
<OptionsSetting value="true" id="Status" />
|
|
58
|
-
<OptionsSetting value="true" id="Edit" />
|
|
59
|
-
<ConfirmationsSetting value="0" id="Add" />
|
|
60
|
-
<ConfirmationsSetting value="0" id="Remove" />
|
|
61
|
-
</component>
|
|
62
|
-
<component name="ProjectReloadState">
|
|
63
|
-
<option name="STATE" value="0" />
|
|
64
|
-
</component>
|
|
65
|
-
<component name="ProjectView">
|
|
66
|
-
<navigator currentView="ProjectPane" proportions="" version="1">
|
|
67
|
-
<flattenPackages />
|
|
68
|
-
<showMembers />
|
|
69
|
-
<showModules />
|
|
70
|
-
<showLibraryContents />
|
|
71
|
-
<hideEmptyPackages />
|
|
72
|
-
<abbreviatePackageNames />
|
|
73
|
-
<autoscrollToSource />
|
|
74
|
-
<autoscrollFromSource />
|
|
75
|
-
<sortByType />
|
|
76
|
-
</navigator>
|
|
77
|
-
<panes>
|
|
78
|
-
<pane id="ProjectPane">
|
|
79
|
-
<subPane>
|
|
80
|
-
<PATH>
|
|
81
|
-
<PATH_ELEMENT>
|
|
82
|
-
<option name="myItemId" value="wrnap" />
|
|
83
|
-
<option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
|
|
84
|
-
</PATH_ELEMENT>
|
|
85
|
-
</PATH>
|
|
86
|
-
</subPane>
|
|
87
|
-
</pane>
|
|
88
|
-
<pane id="Scope" />
|
|
89
|
-
</panes>
|
|
90
|
-
</component>
|
|
91
|
-
<component name="PropertiesComponent">
|
|
92
|
-
<property name="WebServerToolWindowFactoryState" value="false" />
|
|
93
|
-
<property name="options.lastSelected" value="reference.settingsdialog.IDE.editor.colors.Font" />
|
|
94
|
-
<property name="options.splitter.main.proportions" value="0.3" />
|
|
95
|
-
<property name="options.splitter.details.proportions" value="0.2" />
|
|
96
|
-
<property name="options.searchVisible" value="true" />
|
|
97
|
-
<property name="FullScreen" value="false" />
|
|
98
|
-
</component>
|
|
99
|
-
<component name="RunManager">
|
|
100
|
-
<list size="0" />
|
|
101
|
-
</component>
|
|
102
|
-
<component name="ShelveChangesManager" show_recycled="false" />
|
|
103
|
-
<component name="SvnConfiguration">
|
|
104
|
-
<configuration />
|
|
105
|
-
</component>
|
|
106
|
-
<component name="TaskManager">
|
|
107
|
-
<task active="true" id="Default" summary="Default task">
|
|
108
|
-
<changelist id="f215766d-a45c-47cc-a7d7-9487868cd8b4" name="Default" comment="" />
|
|
109
|
-
<created>1399483991383</created>
|
|
110
|
-
<updated>1399483991383</updated>
|
|
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|
-
</task>
|
|
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|
-
<servers />
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-
</component>
|
|
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|
-
<component name="ToolWindowManager">
|
|
115
|
-
<frame x="0" y="22" width="1280" height="774" extended-state="6" />
|
|
116
|
-
<editor active="false" />
|
|
117
|
-
<layout>
|
|
118
|
-
<window_info id="Messages" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.32968536" sideWeight="0.5" order="-1" side_tool="false" content_ui="tabs" />
|
|
119
|
-
<window_info id="Changes" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="-1" side_tool="false" content_ui="tabs" />
|
|
120
|
-
<window_info id="Terminal" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="-1" side_tool="false" content_ui="tabs" />
|
|
121
|
-
<window_info id="TODO" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="6" side_tool="false" content_ui="tabs" />
|
|
122
|
-
<window_info id="Database" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="-1" side_tool="false" content_ui="tabs" />
|
|
123
|
-
<window_info id="Structure" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.25" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" />
|
|
124
|
-
<window_info id="Project" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" weight="0.16796875" sideWeight="0.5" order="0" side_tool="false" content_ui="combo" />
|
|
125
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