bio-gadget 0.4.3 → 0.4.4
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.org +2 -1
- data/lib/bio-gadget.rb +1 -0
- data/lib/bio-gadget/femrg.rb +61 -0
- data/lib/bio-gadget/version.rb +1 -1
- metadata +3 -2
checksums.yaml
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@@ -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: 9bf862ca4bbf3f563456a0285f3e690a08fc2556
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data.tar.gz: 4d4956c35b4d96374d7a73f24b37fe48dc053bfa
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: e3565824e2b4dd2b7cd328e5ade202f350d8edf29e71377e502aaff7402a9266c62f833239d9596b3c2551375b703b5db89e4cb8887acba222b23aef6b41fe89
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data.tar.gz: 4851e1c1047ccc59e4862ba6e965b84f5dc609f926c497e0a9cbc1964bfd4d548961d9a545e5fbbce1906b743cb0cfd309d6c634b2fe846cd3094f6da182460a
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data/README.org
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@@ -16,7 +16,8 @@ Currently available commands are
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- dedup :: Deduplicate fastq (via STDIN)
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- demlt :: Demultiplex fastq by barcodes
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-
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- femrg :: Extract and merge first exons
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- fqxz :: (Re)compression of *.fq(.gz|.bz2) files
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- qvstat :: Statistics of quality values in *.qual file
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- rgt2mtx :: Convert cuffdiff read group tracking file into tab-separated matrix
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- wig5p :: Convert bam-format alignments into wig-format table
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data/lib/bio-gadget.rb
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@@ -0,0 +1,61 @@
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module Bio
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class Gadget < Thor
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desc 'femrg [GTF...]', 'Extract and merge overlapping first exons.'
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def femrg(*gtf_files)
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exon1s = Hash.new
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fp = open("| grep -h '\texon\t' #{gtf_files.nil? ? '-' : gtf_files.join(' ')} | cut -f 1,4,5,7,9")
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fp.each { |line|
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chr, sstart, sstop, str, attr = line.rstrip.split(/\t/)
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exon1s[chr] = Hash.new unless exon1s.key?(chr)
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exon1s[chr][str] = Hash.new unless exon1s[chr].key?(str)
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id = attr.match(/transcript_id \"([^\"]+)\"/).to_a[1]
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en = attr.match(/exon_number \"(\d+)\"/).to_a[1].to_i
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if (!exon1s[chr][str].key?(id) ||
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(str == "+" && en < exon1s[chr][str][id][2]) ||
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(str == "-" && exon1s[chr][str][id][2] < en))
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exon1s[chr][str][id] = [sstart.to_i, sstop.to_i, en]
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end
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}
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fp.close
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idx = 0
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exon1s.each { |chr, exon1schr|
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exon1schr.each { |str, exon1schrstr|
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ids = exon1schrstr.keys.sort { |a, b|
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exon1schrstr[a][0] <=> exon1schrstr[b][0]
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}
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#
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clusters = Array.new
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members = [id = ids.shift]
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start, stop, en = exon1schrstr[id]
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while ids.length > 0
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nid = ids.shift
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nstart, nstop, nen = exon1schrstr[nid]
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if stop < nstart
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clusters.push([members, start, stop])
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members = [nid]
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start = nstart
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stop = nstop
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else
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members.push(nid)
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start, stop = [start, stop, nstart, nstop].sort.values_at(0, 3)
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end
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end
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clusters.push([members, start, stop])
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#
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clusters.each { |members, start, stop|
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attr = "gene_id \"FE#{idx}\"; transcript_id \"FE#{idx}\"; "
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puts [chr, 'bio-gadget:femrg', 'transcript', start, stop, 1000, str, '.', attr].join("\t")
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puts [chr, 'bio-gadget:femrg', 'exon', start, stop, 1000, str, '.', "#{attr}exon_number \"1\"; member_ids \"#{members.join('|')}\""].join("\t")
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idx += 1
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}
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}
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}
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end
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end
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end
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data/lib/bio-gadget/version.rb
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metadata
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: bio-gadget
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version: !ruby/object:Gem::Version
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version: 0.4.
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version: 0.4.4
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platform: ruby
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authors:
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- Shintaro Katayama
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2013-04-
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date: 2013-04-30 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: thor
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@@ -99,6 +99,7 @@ files:
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- lib/bio-gadget.rb
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- lib/bio-gadget/dedup.rb
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- lib/bio-gadget/demlt.rb
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- lib/bio-gadget/femrg.rb
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- lib/bio-gadget/fqxz.rb
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- lib/bio-gadget/qvstat.rb
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- lib/bio-gadget/rgt2mtx.rb
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