fasta_util 0.2.3 → 0.3.0
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- data/VERSION +1 -1
- data/bin/fasta_util +17 -0
- data/fasta_util.gemspec +2 -2
- metadata +3 -3
data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
0.
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1
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+
0.3.0
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data/bin/fasta_util
CHANGED
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@@ -1,6 +1,7 @@
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1
1
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#!/usr/bin/env ruby
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2
2
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require 'thor'
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3
3
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require 'bio'
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4
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+
require 'set'
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4
5
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5
6
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class FastaUtility < Thor
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6
7
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include Thor::Actions
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@@ -88,5 +89,21 @@ class FastaUtility < Thor
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88
89
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puts entry
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89
90
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end
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90
91
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end
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92
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+
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93
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+
desc "composition FILENAME [options]", "Outputs data on the sequence composition"
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94
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+
def composition(filename)
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|
95
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+
invoke :filecheck
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96
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+
composition_hash = Hash[Bio::FlatFile.open(filename).map{|entry| [entry.definition, entry.seq.composition]}]
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|
97
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+
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98
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+
all_chars = composition_hash.values.map{|h| h.keys}.inject(:+).to_set
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|
99
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+
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|
100
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+
puts "definition\t#{all_chars.to_a.join("\t")}"
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|
101
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+
composition_hash.each do |definition, composition|
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102
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+
composition.default = 0
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|
103
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+
print definition, "\t"
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|
104
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+
puts all_chars.map{|char| composition[char]}.join("\t")
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105
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+
end
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106
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+
end
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91
107
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end
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108
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+
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92
109
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FastaUtility.start
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data/fasta_util.gemspec
CHANGED
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@@ -5,11 +5,11 @@
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5
5
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6
6
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Gem::Specification.new do |s|
|
|
7
7
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s.name = %q{fasta_util}
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|
8
|
-
s.version = "0.
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|
8
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+
s.version = "0.3.0"
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9
9
|
|
|
10
10
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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|
11
11
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s.authors = ["robsyme"]
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|
12
|
-
s.date = %q{2011-
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|
12
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+
s.date = %q{2011-05-09}
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|
13
13
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s.default_executable = %q{fasta_util}
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|
14
14
|
s.description = %q{Easy fasta filtering, wrapping, calculating common statistics, sorting etc. Based on the fasta_tool script that I think was written by Jason Stajich.}
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|
15
15
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s.email = %q{rob.syme@gmail.com}
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metadata
CHANGED
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@@ -2,7 +2,7 @@
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|
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2
2
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name: fasta_util
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|
3
3
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version: !ruby/object:Gem::Version
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|
4
4
|
prerelease:
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|
5
|
-
version: 0.
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|
5
|
+
version: 0.3.0
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|
6
6
|
platform: ruby
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|
7
7
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authors:
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8
8
|
- robsyme
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@@ -10,7 +10,7 @@ autorequire:
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10
10
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bindir: bin
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|
11
11
|
cert_chain: []
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|
12
12
|
|
|
13
|
-
date: 2011-
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|
13
|
+
date: 2011-05-09 00:00:00 +08:00
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|
14
14
|
default_executable: fasta_util
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|
15
15
|
dependencies:
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|
16
16
|
- !ruby/object:Gem::Dependency
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@@ -125,7 +125,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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|
|
125
125
|
requirements:
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|
126
126
|
- - ">="
|
|
127
127
|
- !ruby/object:Gem::Version
|
|
128
|
-
hash:
|
|
128
|
+
hash: -421712537586483233
|
|
129
129
|
segments:
|
|
130
130
|
- 0
|
|
131
131
|
version: "0"
|