absee 0.0.0

data/lib/absee.rb

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+# absee
+# 
+# Jenny Cheng 
+# jencheng@ginkgobioworks.com
+#  
+# based off of Abi.cs by Ronaldo Rodrigues Ferreira
+#  
+# extracts the data from ABIF files
+#
+# MIT license 2012
+
+def readAB(filename)
+  #opens ab1 as a File object
+  abFile = open(filename)
+  byteArray = ""
+  #// here we read the first four bytes. It is important
+  #// to remember that we do not seek back the file, just
+  #// because it is not necessary to do this.
+  abFile.seek(0, IO::SEEK_SET)
+  abFile.read(4, byteArray)
+  #ABIF file indicator
+  if byteArray == "ABIF"
+    return processAB(abFile)
+  else
+    return [],[],[],[],[],[]
+  end
+end
+
+def processAB(filestream)
+  #// here, we can read the ABIF header information
+  version = readUnsignedByte_2(4, filestream)
+  #// major versions greater than 1 are not supported
+  #// Applied Biosystems rules
+  if (version / 100 > 1)
+    return [], [], [], [], [], []
+  end
+  #// we just read ABIF, so we don't need more information than that
+  numElements = readUnsignedByte_4(18, filestream)
+  dataOffset = readUnsignedByte_4(26, filestream)
+  directory = readDirectoryEntry(filestream, dataOffset, numElements)
+  numSamples, numBases = gatherInformation(directory, numElements)
+  samples_a, samples_c, samples_g, samples_t = getSamples(filestream, directory, numElements, numSamples)
+  called_sequence = getCalledSequence(filestream, directory, numElements, numBases)
+  peakIndexes = getPeakIndexes(filestream, directory, numElements, numBases)
+  return samples_a, samples_c, samples_g, samples_t, called_sequence, peakIndexes
+end
+
+def readUnsignedByte_2(offset, filestream)
+  #// most significant byte first
+  #// |byte0|byte1| <= |unsigned int|
+  byteArray = ""
+  filestream.seek(offset, IO::SEEK_SET)
+  byteArray = filestream.read(2, byteArray)
+  return (byteArray.getbyte(0) << 8) | byteArray.getbyte(1)
+end
+
+def readUnsignedByte_4(offset, filestream)
+  byteArray = ""
+  filestream.seek(offset, IO::SEEK_SET)
+  byteArray = filestream.read(4, byteArray)
+  #// most significant byte first
+  #// |byte0|byte1|byte2|byte3| <= |unsigned int|
+  return (byteArray.getbyte(0)<<24) | (byteArray.getbyte(1)<<16) | (byteArray.getbyte(2)<<8) | byteArray.getbyte(3)
+end
+
+def readDirectoryEntry(filestream, dataOffset, numElements)
+  filestream.seek(dataOffset, IO::SEEK_SET)
+  byteArray = ""
+  filestream.read(28*numElements, byteArray)
+  directory = []
+  pos = -1
+  
+  
+  #directory structure
+  #[name, tag number, element type, element size, number of elements, data size, data offset]
+  (0..(numElements-1)).each do |i|
+    directory[i] = []
+    #// name
+    name = ""             
+    name << byteArray.getbyte(pos+=1).chr
+    name << byteArray.getbyte(pos+=1).chr
+    name << byteArray.getbyte(pos+=1).chr
+    name << byteArray.getbyte(pos+=1).chr
+    directory[i] << name
+    #// tag number
+    tag_number = byteArray.getbyte(pos+=1)<<24 | byteArray.getbyte(pos+=1)<<16 | byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
+    directory[i] << tag_number
+    #// element type
+    element_type = byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
+    directory[i] << element_type
+    #// element size
+    element_size = byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
+    directory[i] << element_size
+    #// number of elements
+    number_of_elements = byteArray.getbyte(pos+=1)<<24 | byteArray.getbyte(pos+=1)<<16 | byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
+    directory[i] << number_of_elements
+    #// data size
+    data_size = byteArray.getbyte(pos+=1)<<24 | byteArray.getbyte(pos+=1)<<16 | byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
+    directory[i] << data_size
+    #// data offset
+    data_offset = byteArray.getbyte(pos+=1)<<24 | byteArray.getbyte(pos+=1)<<16 | byteArray.getbyte(pos+=1)<<8 | byteArray.getbyte(pos+=1)
+    directory[i] << data_offset
+    #// we do not save the dataHandle field
+    pos += 4;
+  end
+  return directory
+end
+
+
+#directory structure
+#[name, tag number, element type, element size, number of elements, data size, data offset]
+#this is for easier access to the directory element
+def get(array, element)
+  if element == "name"
+    return array[0]
+  elsif element == "tag_number"
+    return array[1]
+  elsif element == "element_type"
+    return array[2]
+  elsif element == "element_size"
+    return array[3]
+  elsif element == "number_of_elements"
+    return array[4]
+  elsif element == "data_size"
+    return array[5]
+  elsif element == "data_offset"
+    return array[6]
+  else
+    return array[0]
+  end
+end
+
+
+def gatherInformation(directory, numElements)
+  numSamples = 0
+  numBases = 0
+  
+  (0..(numElements-1)).each do |i|
+    if (get(directory[i],"name") == "DATA") && (get(directory[i], "tag_number") == 9)
+      numSamples = get(directory[i], "number_of_elements") #number of elements
+    else
+      if (get(directory[i], "name") == "PBAS") && (get(directory[i], "tag_number") == 2)
+        numBases = get(directory[i], "number_of_elements") #number of elements
+      end
+    end
+  end
+  
+  return numSamples, numBases
+end
+
+def getSamples(filestream, directory, numElements, numSamples)
+  samples_a = []
+  samples_c = []
+  samples_g = []
+  samples_t = []
+
+  #// we guess the order being GATC, as Ferreira and Staden does
+  (0..numElements-1).each do |i|
+    tag_number = get(directory[i], "tag_number")
+    if (get(directory[i],"name") == "DATA") && ([9,10,11,12].include? tag_number)
+      byteArray_samples = ""
+      filestream.seek(get(directory[i],"data_offset"), IO::SEEK_SET)
+      filestream.read(get(directory[i], "number_of_elements")*2, byteArray_samples)
+      pos = -1
+      if tag_number == 9 #G
+        (0..numSamples-1).each do |j|
+          value = byteArray_samples.getbyte(pos+=1) << 8 | byteArray_samples.getbyte(pos+=1)
+          samples_g[j] = value
+        end
+      elsif tag_number == 10 #A
+        (0..numSamples-1).each do |j|
+          value = byteArray_samples.getbyte(pos+=1) << 8 | byteArray_samples.getbyte(pos+=1)
+          samples_a[j] = value
+        end
+      elsif tag_number == 11 #T
+        (0..numSamples-1).each do |j|
+          value = byteArray_samples.getbyte(pos+=1) << 8 | byteArray_samples.getbyte(pos+=1)
+          samples_t[j] = value
+        end
+      else #C
+        (0..numSamples-1).each do |j|
+          value = byteArray_samples.getbyte(pos+=1) << 8 | byteArray_samples.getbyte(pos+=1)
+          samples_c[j] = value
+        end
+      end
+    end
+  end
+  return samples_a, samples_c, samples_g, samples_t
+end
+
+def getCalledSequence(filestream, directory, numElements, numBases)
+  calledSequence = []
+  (0..numElements-1).each do |i|
+    if (get(directory[i], "name") == "PBAS") && (get(directory[i], "tag_number") == 2) 
+      byteArray_seq = ""
+      filestream.seek(get(directory[i], "data_offset"))
+      filestream.read(numBases,byteArray_seq)
+      (0..numBases-1).each do |j|
+        calledSequence[j] = byteArray_seq.getbyte(j).chr
+      end
+    end
+  end
+  return calledSequence
+end
+
+def getPeakIndexes(filestream, directory, numElements, numBases)
+  peakIndexes = []
+  (0..numElements-1).each do |i|
+    if (get(directory[i], "name") == "PLOC") && (get(directory[i], "tag_number") == 2)
+      byteArray_peak = ""
+      filestream.seek(get(directory[i], "data_offset"), IO::SEEK_SET)
+      filestream.read(get(directory[i], "number_of_elements")*4, byteArray_peak)
+      pos = -1
+      (0..numBases-1).each do |j|
+        peakIndex = byteArray_peak.getbyte(pos+=1) << 8 | byteArray_peak.getbyte(pos+=1)
+        peakIndexes[j] = peakIndex
+      end
+    end
+  end
+  return peakIndexes
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: absee
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+  prerelease: 
+platform: ruby
+authors:
+- Jenny Cheng
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-04-24 00:00:00.000000000 Z
+dependencies: []
+description: reads ABIF sequencing / chromatogram files and extracts the peak indexes,
+  called sequence, and ACGT values
+email: jencheng@ginkgobioworks.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/absee.rb
+homepage: http://rubygems.org/gems/absee
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: 1.9.3
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: reads .ab1 sequencing/chromatogram files
+test_files: []