mspire 0.7.17 → 0.7.18
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.
data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
0.7.
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1
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+
0.7.18
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@@ -15,9 +15,9 @@ end
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15
15
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DEFAULT_OUTFILE = "quant_compare.tsv"
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16
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17
17
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DEFAULTS = {
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18
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-
:bin_width => Mspire::
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19
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-
:bin_unit => Mspire::
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20
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-
:split => Mspire::
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18
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+
:bin_width => Mspire::Peaklist::DEFAULT_MERGE[:bin_width],
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19
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:bin_unit => Mspire::Peaklist::DEFAULT_MERGE[:bin_unit],
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20
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+
:split => Mspire::Peaklist::DEFAULT_MERGE[:split],
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:round_mz => 6,
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:round_intensity => 6,
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:mz_prefix => "mz"
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@@ -52,8 +52,6 @@ end
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files = ARGV.dup
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55
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-
peaklist = Mspire::PeakList.new
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56
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-
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55
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if opts[:sample_ids]
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basename_to_sample_id = YAML.load_file(opts[:sample_ids])
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end
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@@ -63,25 +61,27 @@ sample_ids = files.map do |filename|
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basename_to_sample_id ? basename_to_sample_id[basename] : basename
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end
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63
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66
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-
peaklists = files.map do |filename|
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64
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+
peaklists = files.zip(sample_ids).map do |filename, sample_id|
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67
65
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putsv "processing: #{filename}"
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68
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-
bunch_of_peaks =
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66
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+
bunch_of_peaks = Mspire::Peaklist.new
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69
67
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Mspire::Mzml.open(filename) do |mzml|
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70
68
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mzml.each_with_index do |spec,i|
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69
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if spec.ms_level == 1
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72
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-
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70
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+
spec.mzs.zip(spec.intensities) do |mz, int|
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71
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bunch_of_peaks.push Mspire::TaggedPeak.new([mz, int], sample_id)
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72
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end
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end
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end
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end
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76
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-
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77
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-
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76
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+
bunch_of_peaks.sort_by!(&:x)
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77
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+
bunch_of_peaks
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end
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putsv "merging peaks"
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share_method = :greedy_y
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#share_method = :share
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84
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-
ar_of_doublets = Mspire::
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84
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+
ar_of_doublets = Mspire::Peaklist.merge_and_deconvolve(peaklists, opts.merge( {:split => share_method, :return_data => true, :have_tagged_peaks => true} ))
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85
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File.open(opts[:outfile],'w') do |out|
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87
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File without changes
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: mspire
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version: !ruby/object:Gem::Version
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4
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-
version: 0.7.
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4
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+
version: 0.7.18
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prerelease:
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platform: ruby
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authors:
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@@ -10,7 +10,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2012-07-
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+
date: 2012-07-17 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: nokogiri
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@@ -332,7 +332,7 @@ files:
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- spec/mspire/mzml/source_file_spec.rb
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333
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- spec/mspire/mzml/spectrum_spec.rb
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334
334
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- spec/mspire/mzml_spec.rb
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335
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-
- spec/mspire/
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335
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+
- spec/mspire/peaklist_spec.rb
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336
336
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- spec/mspire/plms1_spec.rb
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337
337
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- spec/mspire/quant/qspec_spec.rb
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338
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- spec/mspire/spectrum_spec.rb
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@@ -390,7 +390,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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version: '0'
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requirements: []
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rubyforge_project:
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393
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-
rubygems_version: 1.8.
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393
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+
rubygems_version: 1.8.18
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signing_key:
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specification_version: 3
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summary: mass spectrometry proteomics, lipidomics, and tools
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