mspire 0.10.7.2 → 0.10.7.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 7c3d6fd2ccef3ca83f802127523c4518115d55d3
-  data.tar.gz: 99910a0e278af6f0d096c3fb9f06902977681e3b
+  metadata.gz: 8df274039d16839cbdf35f56f1e7ecf32ca47bac
+  data.tar.gz: b5c1d079ff977beca71a96b6ae104eabca0c0d09
 SHA512:
-  metadata.gz: b778a89bbe03de755756a267b772006aa26ced9780384519b194edbb40a2efb54055137e3f5ac81a10044a5d8f53d12ad514b17599d7923cb4bb85b78dc5cf6f
-  data.tar.gz: 0692eef670311afebe4549e8d551ec621c0f5dcc366b7a87e4fa71e129fd165a32fd28293b11e071e99bb7b74787cb9cd4914ba61a77b3d0485f204c05ffe875
+  metadata.gz: 8441a8f5be0b660115d2da8e8c1b738cfecdc3f03aa2611032cf7c346288c25028e47802bc04566d4adb39abd09bbebabd6a37cdc81cd83ef91d7bc28ffd295a
+  data.tar.gz: d9f25609b05e3629d04db3b4906f2323cf1988bb1aa42034f8ba7d2c8f2dba167670d0b9a0b435b15920cd8e91192acdf6668d3379ae41e1c6e1a3fb94ac0341

data/lib/mspire/mzml.rb

@@ -251,7 +251,7 @@ module Mspire
       # @raise [ScanNumbersNotFound] if spectra exist but scan numbers were not
       #   found
       def spectrum_from_scan_num(scan_num)
-        @scan_to_index ||= @index_list[0].create_scan_index
+        @scan_to_index ||= @index_list[0].create_scan_to_index
         raise ScanNumbersNotUnique if @scan_to_index == false
         raise ScanNumbersNotFound if @scan_to_index == nil
         spectrum(@scan_to_index[scan_num])

data/lib/mspire/version.rb

@@ -1,3 +1,3 @@
 module Mspire
-  VERSION = "0.10.7.2"
+  VERSION = "0.10.7.3"
 end

data/script/mzml_to_mgf.rb

@@ -9,7 +9,6 @@ def mascot_charge(val)
   "#{val}#{val > 0 ? '+' : '-'}"
 end
 
-
 opt = {
   filter_zero_intensity: true,
   retention_times: true,
@@ -37,7 +36,7 @@ ARGV.each do |file|
 
   File.open(outfile, 'w') do |out|
     Mspire::Mzml.foreach(file).with_index do |spectrum,i|
-      next unless spectrum.ms_level > 1
+      next unless spectrum.ms_level > 1 && spectrum.mzs.size > 0
       out.puts "BEGIN IONS"
       # id, spectrumid, 
       rt = spectrum.retention_time

data/spec/mspire/mzml_spec.rb

@@ -294,6 +294,12 @@ describe Mspire::Mzml do
         spectrum.mzs[2].should be_within(1e-10).of(164.32693481445312)
       end
 
+      specify '#spectrum_from_scan_num returns a spectrum given a scan number' do
+        # only for files with scan numbers embedded in id with "...scan=<scan_num>..."
+        spectrum = @mzml.spectrum_from_scan_num(2)
+        expect(spectrum.id).to match(/scan=2/)
+      end
+
       specify '#spectrum always returns spectrum with data_processing object (uses default if none given)' do
         @mzml.spectrum(1).data_processing.should be_a(Mspire::Mzml::DataProcessing)
       end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.10.7.2
+  version: 0.10.7.3
 platform: ruby
 authors:
 - John T. Prince
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-05 00:00:00.000000000 Z
+date: 2014-05-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri