dirseq 0.2.1 → 0.3.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/README.md +2 -1
- data/VERSION +1 -1
- data/bin/dirseq +16 -0
- data/spec/script_spec.rb +12 -12
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 48124cb9d1c64721dce10b66a4ae9c6d1773ae5c
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data.tar.gz: 7f7ee356e059956cc204be699d67fab65fa6c41e
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 64263f1b13de9816f978c79961a188f4ab306ff1d7abd0f94d1bfdb6d9c4c807bec7b96b7651afbf1158b2dac38135b6970e273e018bb7f9fdf1fbc9cc736b5e
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data.tar.gz: 6031c1e7952072c0c379a744bf067ae7f2aa9d7328dfec698ed4af84194ac407eb4b18948a3717ef7538f569cdd787a9f0ad4455025ac8148604834c7bb33988
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data/README.md
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@@ -37,7 +37,8 @@ Optional parameters:
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--measure-type TYPE what to count for each gene [options: count, coverage][default: coverage]
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--accepted-feature-types TYPE
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Print only features of these type(s) [default CDS]
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--comment-fields Print elements from the comments in the GFF file [default ID]
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Verbosity:
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-q, --quiet Run quietly, set logging to ERROR level [default INFO]
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data/VERSION
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@@ -1 +1 @@
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1
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0.
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0.3.0
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data/bin/dirseq
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@@ -24,6 +24,7 @@ options = {
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:count_type => COVERAGE_COUNT_TYPE,
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:forward_read_only => false,
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:accepted_feature_types => ['CDS'],
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:comment_fields_to_print => ['ID'],
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}
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o = OptionParser.new do |opts|
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opts.banner = "
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@@ -52,6 +53,10 @@ o = OptionParser.new do |opts|
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"Print only features of these type(s) [default #{options[:accepted_feature_types].join(',')}]") do |arg|
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options[:accepted_feature_types] = Set.new(arg)
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end
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opts.on("--comment-fields", Array,
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"Print elements from the comments in the GFF file [default #{options[:comment_fields_to_print].join(',')}]") do |arg|
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options[:comment_fields_to_print] = arg
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end
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# logger options
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opts.separator "\nVerbosity:\n\n"
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@@ -246,6 +251,9 @@ else
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raise
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end
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headers.push 'annotation'
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options[:comment_fields_to_print].each do |field|
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headers.push field
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end
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puts headers.join("\t")
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covs_fwd.each do |feature, cov_fwd|
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]
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to_print.push cov_rev unless options[:ignore_directions]
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to_print.push product
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options[:comment_fields_to_print].each do |field|
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answer1 = record.attributes.select{|a| a[0] == field}
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if answer1.empty?
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to_print.push ''
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else
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to_print.push answer1[0][1]
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end
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end
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puts to_print.join("\t")
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end
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data/spec/script_spec.rb
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@@ -6,9 +6,9 @@ describe 'script' do
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it "should regular mode" do
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answer = %w(
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contig type start end strand forward_average_coverage reverse_average_coverage annotation
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contig type start end strand forward_average_coverage reverse_average_coverage annotation ID
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).join("\t")+"\n"+%w(
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contig_100 CDS 2 127 + 0.0 1.1428571428571428 unannotated
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contig_100 CDS 2 127 + 0.0 1.1428571428571428 unannotated 40_1
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).join("\t")+"\n"
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found = Bio::Commandeer.run "#{path_to_script} --bam #{data_dir}/eg.bam --gff #{data_dir}/eg.gff -q"
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found = Bio::Commandeer.run "#{path_to_script} --bam #{data_dir}/eg.bam --gff #{data_dir}/eg.gff -q --ignore-direction"
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answer = %w(
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contig type start end strand average_coverage annotation
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contig type start end strand average_coverage annotation ID
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).join("\t")+"\n"+%w(
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contig_100 CDS 2 127 + 1.1428571428571428 unannotated
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contig_100 CDS 2 127 + 1.1428571428571428 unannotated 40_1
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).join("\t")+"\n"
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found.should == answer
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it 'should not fail when the GFF has a FASTA section' do
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answer = %w(
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contig type start end strand forward_average_coverage reverse_average_coverage annotation
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contig type start end strand forward_average_coverage reverse_average_coverage annotation ID
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).join("\t")+"\n"+%w(
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contig_100 CDS 2 127 + 0.0 1.1428571428571428 unannotated
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contig_100 CDS 2 127 + 0.0 1.1428571428571428 unannotated 40_1
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).join("\t")+"\n"
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found = Bio::Commandeer.run "#{path_to_script} --bam #{data_dir}/eg.bam --gff #{data_dir}/eg_with_fasta.gff -q"
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it 'should print annotation out properly' do
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answer = %w(
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contig type start end strand forward_average_coverage reverse_average_coverage annotation
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contig type start end strand forward_average_coverage reverse_average_coverage annotation ID
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).join("\t")+"\n"+%w(
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contig_100 CDS 2 127 + 0.0 1.1428571428571428 putative
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).join("\t")+" methyltransferase YcgJ\n"
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).join("\t")+" methyltransferase YcgJ PROKKA_00001\n"
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found = Bio::Commandeer.run "#{path_to_script} --bam #{data_dir}/eg.bam --gff #{data_dir}/realer.gff -q"
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it 'should print counts correctly' do
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answer = %w(
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contig type start end strand forward_read_count reverse_read_count annotation
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contig type start end strand forward_read_count reverse_read_count annotation ID
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).join("\t")+"\n"+%w(
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contig_100 CDS 2 127 + 0.0 2.0 putative
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).join("\t")+" methyltransferase YcgJ\n"
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).join("\t")+" methyltransferase YcgJ PROKKA_00001\n"
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found = Bio::Commandeer.run "#{path_to_script} --bam #{data_dir}/eg.bam --gff #{data_dir}/realer.gff -q --measure-type count"
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it 'should count only the forward read when asked' do
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answer = %w(
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contig type start end strand forward_read_count reverse_read_count annotation
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contig type start end strand forward_read_count reverse_read_count annotation ID
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).join("\t")+"\n"+%w(
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contig_100 CDS 2 127 + 0.0 1.0 putative
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).join("\t")+" methyltransferase YcgJ\n"
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).join("\t")+" methyltransferase YcgJ PROKKA_00001\n"
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found = Bio::Commandeer.run "#{path_to_script} --bam #{data_dir}/eg.bam --gff #{data_dir}/realer.gff -q --measure-type count --forward-read-only"
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metadata
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--- !ruby/object:Gem::Specification
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name: dirseq
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version: !ruby/object:Gem::Version
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version: 0.
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version: 0.3.0
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platform: ruby
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authors:
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- Ben J. Woodcroft
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2018-
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date: 2018-10-01 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio-commandeer
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