bio-rocker 0.1.02 → 0.1.03
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/bin/ROCker +2 -1
- data/lib/rocker.rb +2 -2
- metadata +1 -1
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: 63b71b4681de7b50aab9c01eb60eed5ce6dc3e7b
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data.tar.gz: 3ec94f33007a8535f77c2878e32bf51d5bc33395
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 29f73a171685a48322299ab1d1c18a470b1a4292cb3aea93a9f52636011e726ceb097aa7f7bdb690cb837fdc7e8b1b64d3ef02b03cc9bda5176cd939fe8e189d
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data.tar.gz: e54a0e01bf15e5b6a054096ac0f8158c7c390fb568d7447cd75c5ffe2e89405ee797ad71afa2667201ef3e9fcf89307d1802e8601abb6737559a81ebce4e770c
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data/bin/ROCker
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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 Mar-23-2015
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#
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require 'rocker'
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@@ -128,6 +128,7 @@ opts = OptionParser.new do |opt|
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opt.on( "--no-transparency", "Do not use (semi-)transparencies."){ |v| o[:transparency] = v }
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opt.on( "--min-score NUMBER", "Minimum Bit-Score to consider a hit. By default: #{ROCker.default :minscore}"){ |v| o[:minscore]=v.to_f }
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opt.on( "--stats-impact", "Plot impact on statistics, instead of absolute values per window."){ o[:impact]=true }
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opt.on( "--stats-ylim", "Limits of the Y-axis in the bottom panel. By default: '-2,.1' if --stats-impact is set, '50,100' otherwise."){ |v| o[:ylim]=v }
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opt.on("-s", "--subject SBJ1,SBJ2,...", Array,
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"Plot only information regarding this(ese) subject(s). If multiple, separate by comma. By default, all hits are plotted."){ |v| o[:sbj]=v }
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opt.on("-f", "--plot-format STRING",
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data/lib/rocker.rb
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@@ -2,7 +2,7 @@
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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 Mar-23-2015
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#
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require 'rocker/blasthit'
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@@ -433,7 +433,7 @@ class ROCker
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puts "Plotting statistics." unless @o[:q]
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data.rrun "par(mar=c(5,4,0,0.5)+.1);"
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data.rrun "plot(1, t='n', xlim=c(0,#{data.aln.cols}),ylim=c(#{@o[:impact] ? "-2,.1" : "50,100"}),xlab='Alignment position (amino acids)',ylab='Precision',xaxs='i');"
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data.rrun "plot(1, t='n', xlim=c(0,#{data.aln.cols}),ylim=c(#{@o[:ylim].nil? ? (@o[:impact] ? "-2,.1" : "50,100") : @o[:ylim]}),xlab='Alignment position (amino acids)',ylab='Precision',xaxs='i');"
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if some_thr
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sn = data.rrun "100*sum(w$tp)/(sum(w$tp)+sum(w$fn))", :float
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sp = data.rrun "100*sum(w$tn)/(sum(w$fp)+sum(w$tn))", :float
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