dirseq 0.0.2 → 0.1.0

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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- data.tar.gz: 7488e7557cd4005dcfc8b6f3c504d4e250434e5b
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data/Gemfile CHANGED
@@ -15,4 +15,5 @@ group :development do
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  gem "jeweler", "~> 2.0"
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  gem "bundler", "~> 1.6"
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  gem "rspec", "~> 2.99"
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+ gem 'pry', '~>0.10'
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  end
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.0.2
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+ 0.1.0
data/bin/dirseq CHANGED
@@ -4,7 +4,6 @@ require 'optparse'
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  require 'bio-logger'
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  require 'bio'
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  require 'bio-commandeer'
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- #require 'pry'
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  require 'set'
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  require 'tempfile'
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@@ -95,12 +94,12 @@ end
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  # Remove the ##FASTA and afterwards from the GFF file as this makes bedtools <2.25 fail
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  # https://github.com/arq5x/bedtools2/issues/235#issuecomment-103776618
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  no_fasta_gff = Tempfile.new('dirseq')
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- Bio::Commandeer.run "sed '/^##FASTA$/,$d' #{gff_file.inspect} > #{no_fasta_gff.path}"
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+ Bio::Commandeer.run "sed '/^##FASTA$/,$d' #{gff_file.inspect} > #{no_fasta_gff.path}", :log => log
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  gff_file = no_fasta_gff.path
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  covs_fwd = nil
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  if options[:ignore_directions]
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- cmd1 = "bedtools coverage -abam #{bam_file.inspect} -b #{gff_file.inspect} -hist"
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+ cmd1 = "bedtools coverage -b #{bam_file.inspect} -a #{gff_file.inspect} -hist"
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  cov_lines_fwd = Bio::Commandeer.run cmd1, :log => log
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  log.info "Parsing coverage profiles"
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  covs_fwd = get_covs.call(cov_lines_fwd)
@@ -109,10 +108,10 @@ else
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  # fwd read 1
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  read1_flag = '-F128' #account for read1 in pair, as well as single reads mapping
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  read2_flag = '-f128'
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- cmdf1 = "samtools view -u #{read1_flag} #{bam_file.inspect} |bedtools coverage -abam /dev/stdin -b #{gff_file.inspect} -hist -s"
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- cmdf2 = "samtools view -u #{read2_flag} #{bam_file.inspect} |bedtools coverage -abam /dev/stdin -b #{gff_file.inspect} -hist -s"
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- cmdr1 = "samtools view -u #{read1_flag} #{bam_file.inspect} |bedtools coverage -abam /dev/stdin -b #{gff_file.inspect} -hist -S"
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- cmdr2 = "samtools view -u #{read2_flag} #{bam_file.inspect} |bedtools coverage -abam /dev/stdin -b #{gff_file.inspect} -hist -S"
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+ cmdf1 = "samtools view -u #{read1_flag} #{bam_file.inspect} |bedtools coverage -b /dev/stdin -a #{gff_file.inspect} -hist -s"
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+ cmdf2 = "samtools view -u #{read2_flag} #{bam_file.inspect} |bedtools coverage -b /dev/stdin -a #{gff_file.inspect} -hist -s"
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+ cmdr1 = "samtools view -u #{read1_flag} #{bam_file.inspect} |bedtools coverage -b /dev/stdin -a #{gff_file.inspect} -hist -S"
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+ cmdr2 = "samtools view -u #{read2_flag} #{bam_file.inspect} |bedtools coverage -b /dev/stdin -a #{gff_file.inspect} -hist -S"
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  command_to_parsed = lambda do |cmds, name|
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  covs_lines_initial = cmds.collect do |cmd|
@@ -122,7 +121,6 @@ else
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  log.info "Parsing #{name}"
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  get_covs.call(lines)
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  end
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- #binding.pry
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  covs = covs_initial[0]
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  covs_initial[1].each do |cov_key, cov|
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  covs[cov_key] += cov
@@ -0,0 +1,3 @@
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+ ##gff-version 3
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+ ##sequence-region contig_100 1 42207
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+ contig_100 Prodigal_v2.60 CDS 2 127 0.5 + 0 ID=PROKKA_00001;eC_number=2.1.1.-;gene=ycgJ_1;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O31474;locus_tag=PROKKA_00001;product=putative methyltransferase YcgJ
data/spec/script_spec.rb CHANGED
@@ -39,4 +39,16 @@ describe 'script' do
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  found.should == answer
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  end
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+
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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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+ ).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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+
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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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+
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+ found.should == answer
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+ end
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  end
metadata CHANGED
@@ -1,14 +1,14 @@
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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: 0.0.2
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+ version: 0.1.0
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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: 2015-06-09 00:00:00.000000000 Z
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+ date: 2016-01-08 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
@@ -142,6 +142,20 @@ dependencies:
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  - - "~>"
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  - !ruby/object:Gem::Version
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  version: '2.99'
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+ - !ruby/object:Gem::Dependency
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+ name: pry
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+ requirement: !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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+ version: '0.10'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !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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+ version: '0.10'
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  description: FPKG (gene expression metric) calculator for metatranscriptomics
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  email: donttrustben near gmail.com
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  executables:
@@ -164,6 +178,7 @@ files:
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  - spec/data/eg.bam
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  - spec/data/eg.gff
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  - spec/data/eg_with_fasta.gff
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+ - spec/data/realer.gff
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  - spec/script_spec.rb
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  - spec/spec_helper.rb
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  homepage: http://github.com/wwood/dirseq
@@ -186,7 +201,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 2.2.2
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+ rubygems_version: 2.4.5.1
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  signing_key:
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  specification_version: 4
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  summary: FPKG calculator for metatranscriptomics