ms-msrun 0.3.1 → 0.3.2

data/History

@@ -1,3 +1,7 @@
+== 0.3.1 / 2011-01-26
+* (since 0.1.1): added support for mzML and parsing zlib compressed spectra
+* added read/write for the .plms1 filetype, an ad hoc binary filetype for ms1 data
+
 == 0.1.1 / 2009-11-19
 * using unified mspire template
 * using spec-more (bacon) rather than minitest-spec

data/VERSION

@@ -1 +1 @@
-0.3.1
+0.3.2

data/bin/ms_to_plms1.rb

@@ -0,0 +1,29 @@
+#!/usr/bin/ruby
+
+require "ms/msrun/plms1"
+
+ext = "plms1"
+
+if ARGV.size == 0
+  puts "usage: #{File.basename(__FILE__)} <file>.mz[X]ML ..."
+  puts "output: <file>.#{ext} ..."
+  puts ""
+  puts "    plms1 is the Prince Lab MS 1 binary file format"
+  puts "    [matlab readers and writers also exist]"
+  puts ""
+  puts "options:"
+  puts "  --spec     print file spec and exit"
+end
+
+if ARGV.include?("--spec")
+  puts Ms::Msrun::Plms1::SPECIFICATION
+  exit
+end
+
+ARGV.each do |file|
+  outfile = file.sub(/\.mzX?ML$/,".#{ext}")
+  Ms::Msrun.open(file) do |ms|
+    # see docs for lots more options here
+    ms.to_plms1.write(outfile)
+  end
+end

data/lib/ms/msrun/plms1.rb

@@ -5,12 +5,25 @@ require 'stringio'
 module Ms
   class Msrun
 
-    def to_plms1
+    # if given scans, will use those, or optionally takes a block where an
+    # array of ms1 scans are yielded and it expects Enumerable scans back.
+    def to_plms1(scans=nil)
       times = []
       scan_numbers = []
       spectra = []
 
-      ms.each(:ms_level => 1, :precursor => false) do |scan|
+      unless scans
+        scans = []
+        ms.each(:ms_level => 1, :precursor => false) do |scan|
+          scans << scan
+        end
+      end
+
+      if block_given?
+        scans = yield(scans)
+      end
+
+      scans.each do |scan|
         times << scan.time
         scan_numbers << scan.num
         spec = scan.spectrum

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 3
-  - 1
-  version: 0.3.1
+  - 2
+  version: 0.3.2
 platform: ruby
 authors: 
 - John T. Prince
@@ -61,6 +61,7 @@ dependencies:
 description: A library for working with LC/MS runs. Part of mspire.  Has parsers for mzXML v1, 2, and 3, mzData (currently broken) and mzML (planned).  Can convert to commonly desired search output (such as mgf).  Fast random access of scans, and fast reading of the entire file.
 email: jtprince@gmail.com
 executables: 
+- ms_to_plms1.rb
 - base64_to_array.rb
 - ms_to_obiwarp.rb
 - ms_to_search.rb
@@ -79,6 +80,7 @@ files:
 - VERSION
 - bin/base64_to_array.rb
 - bin/ms_to_obiwarp.rb
+- bin/ms_to_plms1.rb
 - bin/ms_to_search.rb
 - lib/ms/msrun.rb
 - lib/ms/msrun/axml/mzxml.rb