bio-rocker 1.0.0 → 1.1.9
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- checksums.yaml +4 -4
- data/bin/ROCker +276 -96
- data/lib/rocker.rb +25 -14
- data/lib/rocker/blasthit.rb +8 -5
- data/lib/rocker/genome-set.rb +70 -0
- data/lib/rocker/protein-set.rb +90 -0
- data/lib/rocker/rocdata.rb +26 -9
- data/lib/rocker/rocwindow.rb +20 -18
- data/lib/rocker/step/build.rb +233 -200
- data/lib/rocker/step/compile.rb +11 -6
- data/lib/rocker/step/filter.rb +11 -7
- data/lib/rocker/step/plot.rb +80 -26
- data/lib/rocker/step/search.rb +27 -4
- metadata +16 -14
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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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: ea753ac3675ae8b018f57e1d76fe1a1217a5d329
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data.tar.gz: 00e681953dae2f6dc715e5594f2c2f45cb441e23
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 8fafa5d4adcdf71de47a5f778a94e181a2a1d0d43810a1e4e51b1e37c98e1bf3f2a3932bbf20c27e4ae32c00e6538fdd4ddfa70d695c43d9c731aed35f0aa778
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7
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data.tar.gz: 04e7ecc8213d0050eb4d80ada2badf39b79fe86cb961c1c0999c4c94542aff6e9e877e3a39e69957ad979c5cabe27a4a828f208ebbec9e39f82a9d04ca64c099
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data/bin/ROCker
CHANGED
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@@ -3,7 +3,7 @@
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# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
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# @author Luis (Coto) Orellana
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# @license artistic license 2.0
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# @update
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# @update Sep-07-2015
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#
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lib = File.expand_path(File.dirname(__FILE__) + '/../lib')
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@@ -14,14 +14,20 @@ require 'optparse'
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#================================[ Options parsing ]
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$t = {
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-
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"build" => "Creates in silico metagenomes and training sets from " +
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"reference genomes.",
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"compile" => "Identifies the most discriminant bit-score per alignment " +
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"position in a set of sequence.",
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"search" => "Uses a ROCker compilation to identify reads putatively " +
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"derived from a set of sequences.",
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"filter" => "Uses a pre-compiled set of bit-score thresholds to filter " +
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"a search result.",
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"plot" => "Generates a graphical representation of the alignment, the " +
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"thresholds, and the hits.",
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"info" => "Display additional information about ROCker."
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}
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task = (ARGV.
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ARGV <<
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task = (ARGV.empty? ? "" : ARGV.shift).downcase
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ARGV << "-h" if ARGV.empty? and task != "info"
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o = {}
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opts = OptionParser.new do |opt|
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@@ -32,132 +38,293 @@ opts = OptionParser.new do |opt|
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opt.separator ""
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end
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case task
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when
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when "build"
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unless ROCker.has_build_gems?
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opt.separator "+ UNSATISFIED REQUIREMENTS"
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opt.separator " The building task requires uninstalled gems, please
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opt.separator " The building task requires uninstalled gems, please"
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opt.separator " install them executing:"
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opt.separator " gem install rest_client"
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opt.separator ""
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end
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opt.separator "+ BUILDING ARGUMENTS"
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opt.on("-p", "--positive ID1,ID2,ID3", Array,
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-
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opt.on("-p", "--positive ID1,ID2,ID3", Array,
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"Comma-separated list of UniProtKB IDs corresponding to the positive ",
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"training set. Required unless -P or -a are used."
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){ |v| o[:positive]=v }
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opt.on("-n", "--negative ID1,ID2,ID3", Array,
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"Comma-separated list of UniProtKB IDs corresponding to the negative ",
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"training set. See also -N."){ |v| o[:negative]=v }
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opt.on("-o", "--baseout PATH",
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"Prefix for the output files to be generated. Required."
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){ |v| o[:baseout]=v }
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opt.separator ""
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opt.separator "+ ADVANCED BUILDING ARGUMENTS"
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opt.on("-P", "--positive-file PATH",
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opt.on("-
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opt.on(
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opt.on(
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opt.on("-P", "--positive-file PATH",
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"File containing the positive set, one UniProtKB ID per line.",
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"If used, -p is not required."){ |v| o[:posfile]=v }
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opt.on("-N", "--negative-file PATH",
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"File containing the negative set, one UniProtKB ID per line."
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){ |v| o[:negfile]=v }
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opt.on("-a", "--alignment PATH",
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"Protein alignment of the reference sequences. The defline must have",
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"UniProtKB IDs. If used, -p is not required."){ |v| o[:aln]=v }
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72
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opt.on("-s", "--seqdepth NUMBER",
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73
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"Sequencing depth (reads/bp) to be used in building the in silico" +
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"metagenome.", "By default: '" + ROCker.default(:seqdepth).to_s +
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"'."){ |v| o[:seqdepth]=v.to_f }
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opt.on("-l", "--readlen INTEGER",
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"Average read length of in silico metagenome (in bp).",
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"By default: '" + ROCker.default(:readlen).to_s + "'."
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){ |v| o[:readlen]=v.to_i }
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opt.on("-v", "--overlap INTEGER",
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"Minimum overlap (in bp) with reference gene to tag a positive read.",
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"By default: '" + ROCker.default(:minovl).to_s +
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"'."){ |v| o[:minovl]=v.to_i }
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84
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opt.on("--per-taxon RANK",
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"Use only one genome per taxon to build the metagenome.",
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"Valid ranks include: species, genus, family, order, class, phylum."
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){ |v| o[:pertaxon]=v.downcase }
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opt.on("--nosimulate",
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"Do not simulate metagenome. It implies --nosearch.",
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"By default, metagenome is simulated."){ |v| o[:nosimulate]=v }
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opt.on("--nosearch",
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"Do not execute similarity search. By default it's executed."
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){ |v| o[:nosearch]=v }
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opt.on("--noalignment",
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"Do not align reference set. By default references are aligned."
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){ |v| o[:noaln]=v }
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opt.on("--nocleanup",
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"Keep all intermediate files. By default temporal files are removed."
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){ |v| o[:noclean]=v }
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opt.on("--reuse-files",
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"Re-use existing result files. By default existing files are ignored."
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){ |v| o[:reuse]=true }
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opt.separator ""
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opt.separator "+ EXTERNAL SOFTWARE OPTIONS"
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opt.on(
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-
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opt.on(
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opt.on(
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opt.on("--
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opt.on("--search STR",
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"Similarity search algorithm to use. Supported: blast and diamond",
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"By default: '" + ROCker.default(:search).to_s + "'."
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){ |v| o[:search]=v.to_sym }
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opt.on("--simulator STR",
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"In silico metagenome simulator to use. Supported: grinder.",
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"By default: '" + ROCker.default(:simulator).to_s + "'."
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){ |v| o[:simulator]=v.to_sym }
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opt.on("--aligner STR",
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"Multiple alignment algorithm to use. Supported: clustalo and muscle.",
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"By default: '" + ROCker.default(:aligner).to_s + "'."
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){ |v| o[:aligner]=v.to_sym }
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opt.on("--search-bins PATH",
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"Path to the similarity search executables. By default in $PATH: '" +
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ROCker.default(:searchbins) + "'."
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){ |v| o[:searchbins]=v }
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opt.on("--simulator-bin PATH",
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"Path to the simulator executable. By default in $PATH: '" +
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ROCker.default(:simulatorbin).values.join("' or '") + "'."
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){ |v| o[:simulatorbin]=v }
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opt.on("--aligner-bin PATH",
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"Path to the aligner executable. By default in $PATH: '" +
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ROCker.default(:alignerbin).values.join("' or '") + "'."
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){ |v| o[:alignerbin]=v }
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opt.on("--search-cmd STR",
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"Command for similarity search, where %1$s: binaries, %2$s: program,",
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"%3$s: input, %4$s: database, %5$s: output, %6$d: threads.",
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*ROCker.default(:searchcmd).keys.map do |k|
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["By default if --search #{k}:", "'" +
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ROCker.default(:searchcmd)[k] + "'"]
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end.reduce([],:+) ){ |v| o[:searchcmd]=v }
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opt.on("--makedb-cmd STR",
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"Command calling database formater for similarity search, where",
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"%1$s: binaries, %2$s: dbtype, %3$s: input, %4$s: database.",
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*ROCker.default(:makedbcmd).keys.map do |k|
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["By default if --search #{k}:", "'" +
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ROCker.default(:makedbcmd)[k] + "'"]
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end.reduce([],:+) ){ |v| o[:makedbcmd]=v }
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opt.on("--simulator-cmd STR",
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"Command calling simulator, where %1$s: binary, %2$s: input,",
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"%3$s: seq. depth (X), %4$d: read len., %5$s: output.",
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*ROCker.default(:simulatorcmd).keys.map do |k|
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["By default if --simulator #{k}:", "'" +
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ROCker.default(:simulatorcmd)[k] + "'"]
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end.reduce([],:+) ){ |v| o[:simulatorcmd]=v }
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opt.on("--aligner-cmd STR",
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"Command calling aligner, where %1$s: binary, %2$s: input,",
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"%3$s: output, %4$d: threads.",
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*ROCker.default(:alignercmd).keys.map do |k|
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155
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["By default if --aligner #{k}:", "'" +
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ROCker.default(:alignercmd)[k] + "'."]
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end.reduce([],:+) ){ |v| o[:alignercmd]=v }
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+
when "compile"
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opt.separator "+ COMPILATION ARGUMENTS"
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opt.on("-a", "--alignment PATH",
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opt.on("-a", "--alignment PATH",
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"Protein alignment of the reference sequences. Required."
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){ |v| o[:aln]=v }
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163
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opt.on("-b", "--ref-blast PATH",
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-
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83
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-
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164
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"Tabular BLAST (blastx) of the test reads vs. the reference dataset.",
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"Required unless -T exists."){ |v| o[:blast]=v }
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opt.on("-k", "--rocker PATH",
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"ROCker file to be created. Required."){ |v| o[:rocker]=v }
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+
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84
169
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opt.separator ""
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170
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opt.separator "+ ADVANCED COMPILATION ARGUMENTS"
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opt.on("-
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-
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opt.on("-
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-
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opt.on("-T", "--table PATH",
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"Formated tabular file to be created (or reused).",
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"Required unless -b is provided."){ |v| o[:table]=v }
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174
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opt.on("--min-score NUMBER",
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"Minimum Bit-Score to consider a hit. By default: " +
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ROCker.default(:minscore).to_s){ |v| o[:minscore]=v.to_f }
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opt.on("--norefine",
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"Do not refine windows."){ o[:refine]=false }
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179
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opt.on("-w", "--window INT",
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180
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"Initial size of alignment windows (in number of AA columns). ",
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"By default: " + ROCker.default(:win).to_s + "."
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){ |v| o[:win]=v.to_i }
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183
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opt.on("--reuse-files",
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"Re-use existing result files. By default, existing files are " +
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"ignored."){ |v| o[:reuse]=true }
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opt.separator ""
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187
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opt.separator "+ INPUT/OUTPUT"
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opt.separator " o The input alignment (-a) MUST be in FastA format,
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opt.separator " o The input alignment (-a) MUST be in FastA format, " +
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"and the IDs must"
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94
190
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opt.separator " coincide with those from the BLAST (-b)."
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95
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opt.separator " o The input BLAST (-b) MUST be in tabular format.
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191
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opt.separator " o The input BLAST (-b) MUST be in tabular format. " +
|
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192
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+
"True positives must"
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96
193
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opt.separator " contain the string '@%' somewhere in the query ID."
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97
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-
opt.separator " o The table file (-
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194
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opt.separator " o The table file (-T) should be tab-delimited and " +
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"contain six columns:"
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196
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opt.separator " 1. Subject ID."
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99
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opt.separator " 2. Start of alignment in subject (translated to
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100
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-
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197
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opt.separator " 2. Start of alignment in subject (translated to " +
|
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198
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"alignment column)."
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199
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opt.separator " 3. End of alignment in subject (translated to " +
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"alignment column)."
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101
201
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opt.separator " 4. Bit score."
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102
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opt.separator " 5. A number indicating if it was a true (1) or a
|
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103
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-
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104
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opt.separator "
|
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202
|
+
opt.separator " 5. A number indicating if it was a true (1) or a " +
|
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203
|
+
"false (0) positive."
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204
|
+
opt.separator " 6. Mid-point of the alignment in the reference " +
|
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205
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+
"sequence."
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206
|
+
opt.separator " o The ROCker file (-k) is a tab-delimited file " +
|
|
207
|
+
"containing five columns:"
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105
208
|
opt.separator " 1. First column of the window in the alignment."
|
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106
209
|
opt.separator " 2. Last column of the window in the alignment."
|
|
107
210
|
opt.separator " 3. Number of positives in the window (hits)."
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108
211
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opt.separator " 4. Number of true positives in the window."
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109
212
|
opt.separator " 5. Bit score threshold set for the window."
|
|
110
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-
opt.separator " The file also contains the alignment (commented
|
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213
|
+
opt.separator " The file also contains the alignment (commented " +
|
|
214
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+
"with #:)."
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111
215
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opt.separator ""
|
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112
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-
when
|
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113
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opt.
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opt.on("-
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|
115
|
-
|
|
216
|
+
when "search"
|
|
217
|
+
opt.separator "+ SEARCHING ARGUMENTS"
|
|
218
|
+
opt.on("-k", "--rocker PATH",
|
|
219
|
+
"ROCker file generated by the compile task (-k). " +
|
|
220
|
+
"Required."){ |v| o[:rocker]=v }
|
|
221
|
+
opt.on("-i", "--query PATH",
|
|
222
|
+
"File containing the query sequences in FastA format. " +
|
|
223
|
+
"Required."){ |v| o[:query]=v }
|
|
224
|
+
opt.on("-o", "--out-blast PATH",
|
|
225
|
+
"Filtered tabular BLAST to be created. Required."){ |v| o[:oblast]=v }
|
|
226
|
+
opt.on("-x", "--query-blast PATH",
|
|
227
|
+
"Unfiltered tabular BLAST. By default, this file is not " +
|
|
228
|
+
"kept."){ |v| o[:qblast]=v }
|
|
229
|
+
|
|
116
230
|
opt.separator ""
|
|
117
231
|
opt.separator "+ EXTERNAL SOFTWARE OPTIONS"
|
|
118
|
-
opt.on(
|
|
119
|
-
|
|
120
|
-
|
|
121
|
-
|
|
122
|
-
opt.on(
|
|
123
|
-
|
|
124
|
-
|
|
232
|
+
opt.on("--search STR",
|
|
233
|
+
"Similarity search algorithm to use. Supported: 'blast' and " +
|
|
234
|
+
"'diamond'. By default: '" + ROCker.default(:search).to_s +
|
|
235
|
+
"'.") { |v| o[:search]=v.to_sym }
|
|
236
|
+
opt.on("--search-bins PATH",
|
|
237
|
+
"Path to the similarity search executables. By default in the " +
|
|
238
|
+
"$PATH: '" + ROCker.default(:searchbins) +
|
|
239
|
+
"'.") { |v| o[:searchbins]=v }
|
|
240
|
+
opt.on("--search-cmd STR",
|
|
241
|
+
"Command calling similarity search, where %1$s: binaries, %2$s: " +
|
|
242
|
+
"program, %3$s: input, %4$s: database, %5$s: output, %6$d: threads.",
|
|
243
|
+
*ROCker.default(:searchcmd).keys.map do |k|
|
|
244
|
+
"By default if --search #{k}: '" + ROCker.default(:searchcmd)[k] +
|
|
245
|
+
"'."
|
|
246
|
+
end ){ |v| o[:searchcmd]=v }
|
|
247
|
+
opt.on("--makedb-cmd STR",
|
|
248
|
+
"Command calling database format for similarity search, where %1$s: " +
|
|
249
|
+
"binaries, %2$s: dbtype, %3$s: input, %4$s: database.",
|
|
250
|
+
*ROCker.default(:makedbcmd).keys.map do |k|
|
|
251
|
+
"By default if --search #{k}: '" + ROCker.default(:makedbcmd)[k] +
|
|
252
|
+
"'."
|
|
253
|
+
end ){ |v| o[:makedbcmd]=v }
|
|
254
|
+
when "filter"
|
|
125
255
|
opt.separator "+ FILTERING ARGUMENTS"
|
|
126
|
-
opt.on("-k", "--rocker PATH",
|
|
127
|
-
|
|
128
|
-
|
|
129
|
-
|
|
256
|
+
opt.on("-k", "--rocker PATH",
|
|
257
|
+
"ROCker file generated by the compile task (-k). " +
|
|
258
|
+
"Required."){ |v| o[:rocker]=v }
|
|
259
|
+
opt.on("-x", "--query-blast PATH",
|
|
260
|
+
"Tabular BLAST (blastx) of the query reads vs. the reference " +
|
|
261
|
+
"dataset. Required."){ |v| o[:qblast]=v }
|
|
262
|
+
opt.on("-o", "--out-blast PATH",
|
|
263
|
+
"Filtered tabular BLAST to be created. Required."){ |v| o[:oblast]=v }
|
|
264
|
+
when "plot"
|
|
130
265
|
opt.separator "+ PLOTTING ARGUMENTS"
|
|
131
|
-
opt.on("-k", "--rocker PATH",
|
|
266
|
+
opt.on("-k", "--rocker PATH",
|
|
267
|
+
"ROCker file generated by the compile task (-k). " +
|
|
268
|
+
"Required."){ |v| o[:rocker]=v }
|
|
132
269
|
opt.on("-b", "--ref-blast PATH",
|
|
133
|
-
|
|
134
|
-
|
|
270
|
+
"Tabular BLAST (blastx) of the test reads vs. the reference " +
|
|
271
|
+
"dataset. Required unless -T exists."){ |v| o[:blast]=v }
|
|
272
|
+
opt.on("-o", "--plot-file PATH",
|
|
273
|
+
"File to be created with the plot. By default: value of -k + " +
|
|
274
|
+
"'.' + value of -f."){ |v| o[:gout]=v }
|
|
275
|
+
|
|
135
276
|
opt.separator ""
|
|
136
277
|
opt.separator "+ ADVANCED PLOTTING ARGUMENTS"
|
|
137
|
-
opt.on("-
|
|
138
|
-
|
|
139
|
-
|
|
140
|
-
opt.on(
|
|
141
|
-
opt.on(
|
|
142
|
-
|
|
278
|
+
opt.on("-T", "--table PATH",
|
|
279
|
+
"Formated tabular file to be created (or reused). Required " +
|
|
280
|
+
"unless -b is provided."){ |v| o[:table]=v }
|
|
281
|
+
opt.on("--color", "Color alignment by amino acid."){ o[:color]=true }
|
|
282
|
+
opt.on("--tag-negatives",
|
|
283
|
+
"Mark hits from negative references."){ o[:tag_negatives] = true }
|
|
284
|
+
opt.on("--no-transparency",
|
|
285
|
+
"Do not use (semi-)transparencies."){ |v| o[:transparency] = v }
|
|
286
|
+
opt.on("--min-score NUMBER",
|
|
287
|
+
"Minimum Bit-Score to consider a hit. By default: " +
|
|
288
|
+
ROCker.default(:minscore).to_s + "."){ |v| o[:minscore]=v.to_f }
|
|
289
|
+
opt.on("--stats-impact",
|
|
290
|
+
"Plot impact on statistics, instead of absolute values per " +
|
|
291
|
+
"window."){ o[:impact]=true }
|
|
292
|
+
opt.on("--stats-ylim STRING",
|
|
293
|
+
"Limits of the Y-axis in the bottom panel. By default: '-2,.1' " +
|
|
294
|
+
"if --stats-impact is set, '50,100' otherwise."){ |v| o[:ylim]=v }
|
|
143
295
|
opt.on("-s", "--subject SBJ1,SBJ2,...", Array,
|
|
144
|
-
"Plot only information regarding this(ese) subject(s). If multiple,
|
|
296
|
+
"Plot only information regarding this(ese) subject(s). If multiple, " +
|
|
297
|
+
"separate by comma. By default, all hits are plotted."){ |v| o[:sbj]=v }
|
|
145
298
|
opt.on("-f", "--plot-format STRING",
|
|
146
|
-
"Format of the plot file. Supported values: pdf (default), png,
|
|
147
|
-
|
|
148
|
-
opt.on("-
|
|
299
|
+
"Format of the plot file. Supported values: pdf (default), png, " +
|
|
300
|
+
"jpeg, and tiff."){ |v| o[:gformat]=v }
|
|
301
|
+
opt.on("-W", "--width NUMBER",
|
|
302
|
+
"Width of the plot in inches. By default: " +
|
|
303
|
+
ROCker.default(:width).to_s +
|
|
304
|
+
"."){ |v| o[:width]=v.to_f }
|
|
305
|
+
opt.on("-H", "--height NUMBER",
|
|
306
|
+
"Height of the plot in inches. By default: " +
|
|
307
|
+
ROCker.default(:height).to_s +
|
|
308
|
+
"."){ |v| o[:width]=v.to_f }
|
|
149
309
|
else
|
|
150
310
|
opt.banner = "Usage: ROCker.rb [task] [options]"
|
|
151
311
|
opt.separator ""
|
|
152
312
|
opt.separator "Please specify one of the following tasks:"
|
|
153
313
|
$t.keys.each{ |t| opt.separator " #{t}:\t#{$t[t]}" }
|
|
154
|
-
end
|
|
314
|
+
end # case task
|
|
315
|
+
|
|
155
316
|
opt.separator ""
|
|
156
317
|
opt.separator "+ GENERAL ARGUMENTS"
|
|
157
|
-
opt.on("-
|
|
318
|
+
opt.on("-t", "--threads INT",
|
|
319
|
+
"Number of threads to use. By default: " + ROCker.default(:thr).to_s +
|
|
320
|
+
"."){ |v| o[:thr]=v.to_i }
|
|
321
|
+
opt.on("-R", "--path-to-r PATH",
|
|
322
|
+
"Path to the R executable to be used. By default: '" +
|
|
323
|
+
ROCker.default(:r) + "'."){ |v| o[:r]=v }
|
|
158
324
|
opt.on("-q", "--quiet", "Run quietly."){ |v| o[:q]=true }
|
|
159
|
-
opt.on("-d", "--debug",
|
|
160
|
-
|
|
325
|
+
opt.on("-d", "--debug",
|
|
326
|
+
"Display debugging information."){ |v| o[:debug]=true }
|
|
327
|
+
opt.on("-h", "--help", "Display this screen") do
|
|
161
328
|
puts opt
|
|
162
329
|
exit
|
|
163
330
|
end
|
|
@@ -174,16 +341,29 @@ opts.parse!
|
|
|
174
341
|
rocker = ROCker.new(o)
|
|
175
342
|
begin
|
|
176
343
|
case task
|
|
177
|
-
when
|
|
344
|
+
when "build"
|
|
178
345
|
rocker.build!
|
|
179
|
-
when
|
|
346
|
+
when "compile"
|
|
180
347
|
rocker.compile!
|
|
181
|
-
when
|
|
348
|
+
when "filter"
|
|
182
349
|
rocker.filter!
|
|
183
|
-
when
|
|
350
|
+
when "search"
|
|
184
351
|
rocker.search!
|
|
185
|
-
when
|
|
352
|
+
when "plot"
|
|
186
353
|
rocker.plot!
|
|
354
|
+
when "info"
|
|
355
|
+
puts "ROCker v" + ROCker.VERSION
|
|
356
|
+
puts ""
|
|
357
|
+
puts "If you use ROCker in your research, please cite:"
|
|
358
|
+
puts ROCker.CITATION
|
|
359
|
+
puts ""
|
|
360
|
+
puts "ROCker can be freely used and distributed under the "
|
|
361
|
+
puts "terms of the Artistic License 2.0. See LICENSE.txt."
|
|
362
|
+
puts ""
|
|
363
|
+
puts "For additional information and documentation, visit:"
|
|
364
|
+
puts "http://enve-omics.ce.gatech.edu/rocker/"
|
|
365
|
+
puts "For our list of curated models, visits:"
|
|
366
|
+
puts "http://enve-omics.ce.gatech.edu/rocker/models"
|
|
187
367
|
end
|
|
188
368
|
rescue => err
|
|
189
369
|
$stderr.puts "Exception: #{err}\n\n"
|