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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require 'thor'
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require 'bio'
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4
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+
require 'set'
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class FastaUtility < Thor
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include Thor::Actions
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@@ -88,5 +89,21 @@ class FastaUtility < Thor
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puts entry
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end
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end
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+
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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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all_chars = composition_hash.values.map{|h| h.keys}.inject(:+).to_set
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+
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puts "definition\t#{all_chars.to_a.join("\t")}"
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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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print definition, "\t"
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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
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end
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108
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+
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92
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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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Gem::Specification.new do |s|
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s.name = %q{fasta_util}
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8
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-
s.version = "0.
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8
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+
s.version = "0.3.0"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["robsyme"]
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-
s.date = %q{2011-
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s.date = %q{2011-05-09}
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s.default_executable = %q{fasta_util}
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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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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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name: fasta_util
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version: !ruby/object:Gem::Version
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prerelease:
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-
version: 0.
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5
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+
version: 0.3.0
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platform: ruby
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authors:
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- robsyme
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@@ -10,7 +10,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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date: 2011-
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date: 2011-05-09 00:00:00 +08:00
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default_executable: fasta_util
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dependencies:
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- !ruby/object:Gem::Dependency
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@@ -125,7 +125,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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-
hash:
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128
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+
hash: -421712537586483233
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segments:
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- 0
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version: "0"
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