diadem 0.0.3 → 0.0.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 2f637d86e13f2cadb95b2eae228c4a2ac4e7a9aa
-  data.tar.gz: c44c5804cb1b5d1120e50be0f794a5f4bb0d8a19
+  metadata.gz: 6fa16a3c524c7225ef4f4be890f0b1af8073bd7d
+  data.tar.gz: 927b682e29c08ae8bae24be3f10a1e73fa1d8977
 SHA512:
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+  metadata.gz: 2106d9d8d5811d48b213e0798e5c2066c16a3f8e8667b103362a3c72b6248f0e6a728b4c72e7e75ece5ac84a5fa222b82d9dc22050b1689559529a1cc2ede63b
+  data.tar.gz: 81b9d70759379eedc3adb9854e05d6782a926fd204bead5ea88a1c19a583807150140777a2a54752326eb627657eba0c687ee99db5fede5e1287e1a81053c54e

data/lib/diadem/cubic.rb

@@ -31,7 +31,8 @@ module Diadem
           isotopomers = *opt.num_isotopomers.times.map {|n| "M#{n}" }
           cats.push(*isotopomers)
           isotopomers.each do |label|
-            (opt.degree).downto(0) do |coeff|
+            lowest_coeff = opt.return_zero_coeff ? 0 : 1
+            (opt.degree).downto(lowest_coeff) do |coeff|
               cats << [label, "coeff", coeff].join("_")
             end
           end
@@ -39,6 +40,7 @@ module Diadem
         end
 
         aaseqs.compact!  # ignore blank lines
+        aaseqs.uniq! if opt.remove_duplicates
 
         aaseqs.each do |aaseq|
           # we cannot ensure the base 0% has been included in the range, so
@@ -69,7 +71,9 @@ module Diadem
           line = [aaseq, modinfo, info.formula, info.formula.mass.round(6), info.penetration]
           line.push *zero_pct_dist.intensities[0,opt.num_isotopomers].map {|v| v.round(6) }
           polynomials.each do |coeffs|
-            line.push *coeffs.reverse
+            rev_coeffs = coeffs.reverse
+            rev_coeffs.pop unless opt.return_zero_coeff
+            line.push *rev_coeffs
           end
           out.puts line.join(opt.delim)
         end

data/lib/diadem/cubic/commandline.rb

@@ -22,6 +22,8 @@ module Diadem
             degree: 3,
             header: true,
             num_isotopomers: 5,
+            zero: false,
+            remove_duplicates: true,
           } )
                               
           parser = OptionParser.new do |op|
@@ -37,11 +39,13 @@ module Diadem
             op.separator "options:"
             op.on("-e", "--element <#{opt.element}>", "element with isotopic label") {|v| opt.element = v.to_sym }
             op.on("-m", "--mass-number <#{opt.mass_number}>", Integer, "the labeled element mass number") {|v| opt.mass_number = v }
-            op.on("--no-carbamidomethyl", "do not use this mod by default") { opt.carbamidomethyl = false }
+            op.on("--[no-]carbamidomethyl", "default: carbamidomethyl = true") {|v| opt.carbamidomethyl = v }
             op.on("--range <start:stop:step>", "the underlying input values (#{[start, stop, step].join(':')})") {|v| opt.range = make_range[ *v.split(':') ] }
             op.on("--degree <#{opt.degree}>", Integer, "the degree polynomial") {|v| opt.degree = v }
             op.on("--num-isotopomers <#{opt.num_isotopomers}>", Integer, "the number of isotopomers to calculate") {|v| opt.num_isotopomers = v }
-            op.on("--no-header", "don't print a header line") {|v| opt.header = false }
+            op.on("--[no-]header", "print header line, default: true") {|v| opt.header = v }
+            op.on("--return-zero-coeff", "return the 0th polyfit coefficient") {|v| opt.return_zero_coeff = v }
+            op.on("--[no-]remove-duplicates", "disregard duplicate peptide entries, default: true") {|v| opt.remove_duplicates = v }
           end
           parser.parse!(argv)
           if argv.size == 0

data/lib/diadem/version.rb

@@ -1,3 +1,3 @@
 module Diadem
-  VERSION = "0.0.3"
+  VERSION = "0.0.4"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: diadem
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors:
 - John Prince
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-29 00:00:00.000000000 Z
+date: 2013-11-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: mspire