lsa 0.1.0 → 0.1.1

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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data/lib/lsa.rb CHANGED
@@ -4,26 +4,24 @@ require "abort_if"
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  include AbortIf
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-
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-
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-
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  module Lsa
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-
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  def clean_str str
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  str.strip.gsub(/[^\p{Alnum}_]+/, "_").gsub(/_+/, "_")
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  end
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-
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  def parse_mapping_file mapping_fname, mmseqs_final_outf
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  data_labels = []
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  label2outf = {}
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  doc2new_doc = {}
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  File.open(mapping_fname, "rt").each_line.with_index do |line, idx|
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  if idx.zero?
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- curren_label, *data_labels = line.chomp.split("\t").map do |str|
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+ current_label, *data_labels = line.chomp.split("\t").map do |str|
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  clean_str str
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  end
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+ abort_if data_labels.any? { |label| label == "original" },
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+ "Illegal data label: 'original'. Please change it."
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+
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  abort_unless data_labels.uniq.count == data_labels.count,
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  "The data labels are not unique in #{mapping_fname}"
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@@ -1,3 +1,3 @@
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  module Lsa
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- VERSION = "0.1.0"
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+ VERSION = "0.1.1"
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  end
@@ -0,0 +1,4 @@
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+ file name group original
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+ e_coli.faa.gz bacteria a
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+ m_mazei.faa.gz archaea a
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+ s_flexneri.faa.gz bacteria b
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: lsa
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  version: !ruby/object:Gem::Version
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- version: 0.1.0
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+ version: 0.1.1
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  platform: ruby
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  authors:
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  - Ryan Moore
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  autorequire:
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  bindir: exe
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  cert_chain: []
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- date: 2017-07-23 00:00:00.000000000 Z
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+ date: 2017-08-10 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: abort_if
@@ -109,14 +109,13 @@ files:
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  - lib/lsa.rb
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  - lib/lsa/version.rb
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  - lsa.gemspec
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- - test_files/#cluster_file.txt#
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- - test_files/.#cluster_file.txt
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  - test_files/cluster_file_another_group.txt
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  - test_files/cluster_file_group.txt
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  - test_files/cluster_file_original.txt
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  - test_files/e_coli.faa.gz
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  - test_files/m_mazei.faa.gz
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  - test_files/mapping.txt
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+ - test_files/mapping_with_bad_group_name.txt
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  - test_files/s_flexneri.faa.gz
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  - test_files/small/e_coli.faa.gz
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  - test_files/small/m_mazei.faa.gz
@@ -1,3 +0,0 @@
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- e_coli_faa_gz~orf_1 e_coli_faa_gz~orf_1
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- e_coli_faa_gz~orf_1 m_mazei_faa_gz~orf_1
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- e_coli_faa_gz~orf_1 s_flexneri_faa_gz~orf_1
@@ -1 +0,0 @@
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- test_files/moorer@roaming-254-155.host.udel.edu.943