protk 1.2.6.pre5 → 1.3.0.pre1

data/lib/protk/protein_annotator.rb

@@ -1,646 +0,0 @@
-require 'rubygems'
-require 'spreadsheet'
-require 'protk/swissprot_database'
-require 'protk/bio_sptr_extensions'
-require 'protk/protxml'
-require 'protk/spreadsheet_extensions'
-require 'protk/biotools_excel_converter'
-require 'protk/plasmodb'
-require 'protk/constants'
-
-
-class ProteinAnnotator < Object
-
-
-  def initialize()
-      @genv = Constants.new()
-  end
-  
-  def env
-    return @genv
-  end
-  
-  def outputBookFromExcelInput(inputFile,numrows=0)
-    
-     # Open the original excel workbook for reading
-     inputBook = Spreadsheet.open "#{inputFile}"
-
-     return inputBook.copyBook(numrows)
-
-  end
-  
-  
-  
-  # Combines results from prot and pep xml files
-  # 
-  def outputBookFromProtXMLAndPepXML(inputFileProt,inputFilePep,numrows=0)
-    protxml=ProtXML.new(inputFileProt)
-
-    # By default here we don't report anything with a probability less than 0.6
-    # This should be a user parameter someday
-    #
-    rows=protxml.as_rows(0.6) 
-
-    # Figure out how many rows to convert if not specified
-    #
-    if ( numrows==0 || numrows >= rows.length)
-      numrows=rows.length
-    else
-      rows=rows[0...numrows]
-    end
-
-
-
-    # Create a new workbook from scratch for writing
-    outputBook = Spreadsheet::Workbook.new
-    outputSheet = outputBook.create_worksheet
-
-    rows.reverse!
-
-    rows.each { |row| 
-      outputSheet.insert_row(0,row)
-    }
-        
-    outputBook
-  end
-  
-  
-  
-  
-  # Takes a prot.xml file as input and returns an excel workbook with a single column containing the Accessions of proteins in the file
-  # The header of the accessions column will be 'Accessions'
-  # If a protein has 'indistinguishable proteins' each of those is given a separate line
-  #
-  # Throws an error if no proteins could be found in the prot.xml file
-  # In addition to the Accessions column, other information will be extracted from the file including
-  # 1. A list of indistinguishable proteins
-  # 2. The number of peptides on which the ID was based
-  # 3. The protein probability
-  # 4. A ; separated list of peptides on which the ID is based
-  # 5. Percent coverage for the protein
-  # 
-  def outputBookFromProtXML(inputFile,numrows=0)
-    protxml=ProtXML.new(inputFile)
-
-    # By default here we don't report anything with a probability less than 0.6
-    # This should be a user parameter someday
-    #
-    rows=protxml.as_rows(0.6) 
-
-    # Figure out how many rows to convert if not specified
-    #
-    if ( numrows==0 || numrows>=rows.length)
-      numrows=rows.length
-    else
-      rows=rows[0...numrows]
-    end
-
-
-
-    # Create a new workbook from scratch for writing
-    outputBook = Spreadsheet::Workbook.new
-    outputSheet = outputBook.create_worksheet
-
-    rows.reverse!
-
-    rows.each { |row| 
-      outputSheet.insert_row(0,row)
-    }
-        
-    outputBook
-  end
-  
-  
-  
-  
-  
-  
-  
-  # Takes a biotools outputted excel file and produces an excel workbook with a single Accessions column of proteins
-  #
-  def outputBookFromBiotoolsExcel(inputFile,numrows=0)
-    converter=BioToolsExcelConverter.new(inputFile)
-    rows=converter.get_rows
-        
-    # Create a new workbook from scratch for writing
-    outputBook = Spreadsheet::Workbook.new
-    outputSheet = outputBook.create_worksheet
-
-    rows.reverse!
-
-    rows.each { |row| 
-      outputSheet.insert_row(0,row)
-    }
-        
-    outputBook
-    
-    
-  end
-  
-  # Takes a WarpLC Protein List file as input and returns an excel workbook with a single column containing the Accessions of proteins in the file
-  # The header of the accessions column will be 'Accessions'
-  # Throws an error if no proteins could be found in the WarpLC file .. this could also happen if the file is the wrong format
-  # 
-  def outputBookFromWarpLCInput(inputFile,numrows=0)
-    file=File.new(inputFile)
-    xmldoc=REXML::Document.new(file)
-    accessions=REXML::XPath.match(xmldoc,"//ProteinReport/Protein")
-    if ( accessions==nil )
-      throw "No proteins found in the WarpLC Proteinlist file #{inputFile}"
-    end
-    accessions=accessions.collect { |el| el.attributes['Accession']}
-    accessions.insert(0,"Accession")
-
-    # Figure out how many rows to convert if not specified
-    if ( numrows==0 || numrows>accessions.length)
-      numrows=accessions.length+1
-    else
-      accessions=accessions[0...numrows]
-    end
-
-
-
-    # Create a new workbook from scratch for writing
-    outputBook = Spreadsheet::Workbook.new
-    outputSheet = outputBook.create_worksheet
-
-    outputSheet.insert_column(accessions,0)
-    
-    outputBook
-  end
-  
-  # First looks at the file extension. If it is xls then filetype 'xls' is returned. 
-  # Otherwise, we assume the file is XML
-  #
-  def isExcelFile(fileName,input_type)
-    if ( input_type=="excel")
-      return true
-    end
-    
-    ext=fileName.split(".").last
-    if(ext=="xls")
-      return true
-    end
-    return false
-  end
-  
-  def isProtXMLFile(fileName,input_type)
-    if ( input_type=="protXML")
-      return true
-    end
-    
-    
-    if ( fileName.match(/\.prot\.xml$/) != nil )
-      return true
-    else
-      return false
-    end
-  end
-  
-  def isBioToolsFile(fileName,input_type)    
-    BioToolsExcelConverter.isBiotools(fileName)
-  end
-  
-  # Given a worksheet with a column called 'Status' change true values to 'Validated' and false values to 'Potential'
-  def renameValuesInColumn(workSheet,colIndex,from,to)
-    workSheet.rows.each { |row| 
-      if ( row[colIndex]==from)
-        row[colIndex]=to
-      end
-    }
-  end
-  
-  def hasAccession(row)
-    hasit=false
-    row.each do|cell|
-      if (cell.to_s=="Accession")
-        hasit=true
-      end
-    end
-    hasit
-  end
-  
-  def row_is_empty(row)
-    isempty=true
-    if (row==nil)
-      return true
-    end
-    
-    row.each do |cell|
-      if ( cell!=nil && cell.to_s!="")
-        isempty=false
-      end
-    end
-    isempty
-  end
-  
-  def convert(inputFile,outputFile,input_type=nil,output_type="xls",numrows=0,accessionColumnName="Accession",entrezIDColumnName="Entrez.ID",hiddenColumns=[])
-
-    @genv.log("Converting #{inputFile} to #{outputFile}",:info)
-
-    Spreadsheet.client_encoding = 'UTF-8'   
-    
-    
-    case true
-    when isExcelFile(inputFile,input_type)
-      @genv.log("Excel file was biotools",:info)      
-      if ( isBioToolsFile(inputFile,input_type))
-        outputBook=outputBookFromBiotoolsExcel(inputFile,numrows)
-      else
-        @genv.log("Excel file was non biotools",:info)
-        outputBook=outputBookFromExcelInput(inputFile,numrows)
-      end
-      outputSheet=outputBook.worksheet 0
-    when isProtXMLFile(inputFile,input_type)
-      @genv.log("Got a Prot XML File as Input",:info)
-      outputBook=outputBookFromProtXML(inputFile,numrows)
-      outputSheet=outputBook.worksheet 0      
-    else      
-      @genv.log("File is not prot.xml or excel .. trying WarpLCResult",:info)
-      outputBook=outputBookFromWarpLCInput(inputFile,numrows)
-      outputSheet=outputBook.worksheet 0
-    end
-    
-    # Chop off and save any rows prior to the header and remove any empty rows
-    #
-    rows_for_deletion=[]
-    header_row=nil
-    keep_rows=[]
-    rowi=0
-    outputSheet.each do |row|
-      
-      if ( !row_is_empty(row) && header_row==nil && hasAccession(row))
-        header_row=rowi
-      end
-
-      if (row_is_empty(row) || header_row==nil)
-        rows_for_deletion.push(rowi)
-      end
-      
-      if (header_row==nil)
-        keep_rows.push(row)
-      end
-      rowi=rowi+1
-    end
-        
-    deletion_index=0
-    rows_for_deletion.each do |i|
-      outputSheet.delete_row(i-deletion_index)
-      deletion_index=deletion_index+1
-    end    
-    
-    header=outputSheet.row 0
-    lastcolIndex=0
-    accessionColumn=nil
-
-    # Grab the accession column
-    for i in 0...header.length
-      if ( header[i]==accessionColumnName)
-        accessionColumn=outputSheet.column i
-        accessionColumnIndex=i
-      end
-      if ( header[i]=="" && lastcolIndex==0)
-        lastcolIndex=i
-      end
-
-      if ( header[i]=="OK")
-        header[i]="Status"
-        renameValuesInColumn(outputSheet,i,"true","Validated")
-        renameValuesInColumn(outputSheet,i,"false","Contaminant")
-      end
-      
-    end
-
-    # If we didn't find an empty column then just set lastcolIndex to i
-    if ( lastcolIndex==0)
-      lastcolIndex=i
-    end
-    
-    if ( accessionColumn==nil) 
-      throw "No Accession column in input excel file. One column must have the header 'Accession'"
-    end
-    
-    ids = accessionColumn.collect { |id| 
-      if ( id!=nil)
-        id
-      else
-        ""
-      end
-    }
-    # Remove the 0th value because it is the header
-    ids.delete_at(0)
-
-    #### Now grab some additional column information from uniprot ####
-
-    # Create a Hash with keys corresponding to the keys returned by uniprot.parse and with values corresponding to arrays of column values
-    # We start the columns off with the header name
-    newColumns={'recname'=>["Primary Name"],'cd'=>["CD Antigen Name"],'altnames'=>["Alternate Names"], 
-      'location' => ["Subcellular Location"],
-      'function' => ["Known Function"],
-      'similarity' => ["Similarity"],
-      'tissues' => ["Tissue Specificity"],
-      'disease' => ["Disease Association"],
-      'domain' => ["Domain"],
-      'subunit' => ["Sub Unit"],
-      'nextbio' => ["NextBio"],
-      'ipi' => ["IPI"],
-      'intact' => ["Interactions"],
-      'pride' => ['Pride'],
-      'ensembl'=> ['Ensembl'],
-      'num_transmem'=>["Transmembrane Regions"],
-      'signalp'=>['Signal Peptide']
-    }
-
-    newColumnKeys=['recname','cd','altnames','location','function','similarity','tissues','disease','domain','subunit','nextbio','ipi','intact','pride','ensembl','num_transmem','signalp']
-
-
-    #    xmlurls=accs.collect {|acc| uniprot.entry_url_for_accession(acc,'xml') }
-
-    @genv.log("Initializing database",:info)
-
-    swissprotdb=SwissprotDatabase.new(@genv)
-    @genv.log("Retrieving data for #{ids.length} entries from Swissprot database ",:info)
-    accs=[]
-    plasmodbids=[]
-    found_plasmodb_ids=false
-    
-    $stdout.putc "\n"
-    ids.each { |uniprot_id| 
-
-      $stdout.putc "."
-      $stdout.flush
-
-      sptr_entry=swissprotdb.get_entry_for_name(uniprot_id)
-
-
-      if ( sptr_entry==nil)
-        @genv.log("No entry for #{uniprot_id} in uniprot database",:warn)
-        newColumnKeys.each { |key| newColumns[key].push("") }
-        accs.push("")
-        
-        # Bit of a hack. If the id is not sp and not decoy we assume it is plasmodb
-        #
-        if ( uniprot_id=~/^decoy_/)
-        else
-          plasmodbids.push(uniprot_id)
-          found_plasmodb_ids=true 
-        end
-        
-      else
-        accs.push(sptr_entry.accession)
-        plasmodbids.push("")
-        
-        newColumnKeys.each { |key|     
-            
-          val=sptr_entry.send(key)
-          if ( val==nil)
-            str=""
-          elsif ( val.class==Array)
-            str=val.join(";")
-          else
-            str=val.to_s
-          end
-          newColumns[key].push(str)
-        }
-      end
-    }
-    $stdout.putc "\n"
-    
-    
-    # Trying PlasmoDB for unknown IDs
-    #
-    if ( found_plasmodb_ids  ) 
-      $stdout.putc "Searching PlasmoDB for unknown Id's\n"
-      @genv.log "Searching PlasmoDB for unknown Id's", :info
-
-      plasmodb = PlasmoDB.new(@genv)
-
-      row_index=1 # Starts from 1 because of the header
-      
-      plasmodbids.each { |plasmodb_id| 
-        
-        if ( plasmodb_id!="")
-          p plasmodb_id
-        
-          plasmodb_entry = plasmodb.get_entry_for_name(plasmodb_id)
-        
-          if ( plasmodb_entry != nil )
-
-#             newColumnKeys=['recname','cd','altnames','location','function','similarity','tissues','disease','domain','subunit','nextbio','ipi','intact','pride','ensembl','num_transmem','signalp']
-
-            newColumns['recname'][row_index]=plasmodb_entry['Product Description']
-            
-            if ( plasmodb_entry['Annotated GO Component']!="null" )
-              newColumns['location'][row_index]=plasmodb_entry['Annotated GO Component']
-            else 
-              newColumns['location'][row_index]=plasmodb_entry['Predicted GO Component']
-            end
-            
-            if ( plasmodb_entry['Annotated GO Function'] !="null" )
-              newColumns['function'][row_index]=plasmodb_entry['Annotated GO Function']
-            else
-              newColumns['function'][row_index]=plasmodb_entry['Predicted GO Function']              
-            end
-            
-            newColumns['signalp'][row_index]=plasmodb_entry['SignalP Peptide']
-            
-            newColumns['num_transmem'][row_index] = plasmodb_entry['# TM Domains']
-
-          end
-        end
-
-        row_index=row_index+1
-
-        
-      }
-      
-      
-    end
-    
-    
-    @genv.log("Done",:info)
-    
-    newColumnKeys.reverse.each { |key| 
-      outputSheet.insert_column(newColumns[key],lastcolIndex)
-    }
-
-    # Now hide some columns
-    hide=hiddenColumns
-    for i in 0...outputSheet.row(0).length
-      if ( hide.detect { |h| header[i].include?(h)} !=nil)
-        outputSheet.column(i).hidden=TRUE
-        accessionColumn=outputSheet.column i
-        accessionColumnIndex=i
-      end
-      if ( header[i]=="" && lastcolIndex==0)
-        lastcolIndex=i
-      end
-    end
-
-
-    # Now add hyperlinks to various columns
-    @genv.log("Creating Hyperlinks",:info)
-
-    # Figure out column indexes for all the hyperlinked columns
-    header=outputSheet.row 0
-    
-    entrezIDColumn=nil
-    
-    
-    # Grab the column indexes of existing columns to be hyperlinked
-    for i in 0...header.length
-      if ( header[i]==accessionColumnName )
-        accessionColumnIndex=i
-      end
-      if ( header[i]=="IPI")
-        ipiColumnIndex=i
-      end
-      if ( header[i]=="Interactions")
-        intactColumnIndex=i
-      end
-      if ( header[i]=="Pride")
-        prideColumnIndex=i
-      end
-      if ( header[i]=="Ensembl")
-        ensemblColumnIndex=i
-      end
-      if ( header[i]=="NextBio")
-        nextbioColumnIndex=i
-      end
-      
-      if (header[i]==entrezIDColumnName)
-        entrezIDColumnIndex=i
-        entrezIDColumn=outputSheet.column i
-        entrezIDs=entrezIDColumn.collect { |id| id }
-      end
-      
-    end
-
-
-    # Create a format for the hyperlinks
-    hyperlink_format = Spreadsheet::Format.new({:color => :blue,:weight => :bold,:size => 10})
-
-    # Add hyperlink format to the appropriate columns
-    outputSheet.column(accessionColumnIndex).default_format=hyperlink_format
-    outputSheet.column(nextbioColumnIndex).default_format=hyperlink_format
-    outputSheet.column(ipiColumnIndex).default_format=hyperlink_format
-    outputSheet.column(intactColumnIndex).default_format=hyperlink_format
-    outputSheet.column(prideColumnIndex).default_format=hyperlink_format
-    outputSheet.column(ensemblColumnIndex).default_format=hyperlink_format
-
-    if ( entrezIDColumn!=nil)
-      outputSheet.column(entrezIDColumnIndex).default_format=hyperlink_format
-    end
-    
-    # Create all the hyperlinks
-    for rowi in 1...outputSheet.rows.length do
-
-      if ( plasmodbids[rowi-1]!="")
-        # Assume plasmodb .. and use plasmodb url
-        outputSheet.row(rowi)[accessionColumnIndex]=Spreadsheet::Link.new(url="http://www.plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&project_id=&primary_key=#{ids[rowi-1]}",description=plasmodbids[rowi-1]) 
-      else 
-        # Otherwise assume sp
-        outputSheet.row(rowi)[accessionColumnIndex]=Spreadsheet::Link.new(url="http://www.uniprot.org/uniprot/#{accs[rowi-1]}.html",description=ids[rowi-1]) 
-      end
-      
-      outputSheet.row(rowi)[nextbioColumnIndex]=Spreadsheet::Link.new(url="http://www.nextbio.com/b/home/home.nb?id=#{newColumns['nextbio'][rowi]}&type=feature",description=newColumns['nextbio'][rowi])
-      outputSheet.row(rowi)[ipiColumnIndex]=Spreadsheet::Link.new(url="http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=#{newColumns['ipi'][rowi]}",description=newColumns['ipi'][rowi])
-      outputSheet.row(rowi)[intactColumnIndex]=Spreadsheet::Link.new(url="http://www.ebi.ac.uk/intact/pages/interactions/interactions.xhtml?query=#{newColumns['intact'][rowi]}*",description=newColumns['intact'][rowi])
-      outputSheet.row(rowi)[prideColumnIndex]=Spreadsheet::Link.new(url="http://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=#{newColumns['pride'][rowi]}",description=newColumns['pride'][rowi])
-      outputSheet.row(rowi)[ensemblColumnIndex]=Spreadsheet::Link.new(url="http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=#{newColumns['ensembl'][rowi]}",description=newColumns['ensembl'][rowi])
-      outputSheet.row(rowi).height=24
-
-  
-      if ( entrezIDColumn!=nil && entrezIDs[rowi]!=nil)
-        outputSheet.row(rowi)[entrezIDColumnIndex]=Spreadsheet::Link.new(url="http://www.ncbi.nlm.nih.gov/gene/#{entrezIDs[rowi].to_i.to_s}",description=entrezIDs[rowi].to_i.to_s)
-      end
-
-    end
-        
-    # Change the names of any columns to nicer values if you need to
-    #
-    outputSheet.row(0)[accessionColumnIndex]="Uniprot Link"
-    
-    if ( entrezIDColumn!=nil)
-      outputSheet.row(0)[entrezIDColumnIndex]="Entrez.ID"
-    end
-    
-    
-    
-    # Having hyperlinked existing columns we now add any additional columns (hyperlinks based on existing data)
-    # Note that all the column indexes will now be invalid which is why this is done near the end
-    #
-    
-    # Insert an entrez ID based iHOP literature search link if possible
-    if ( entrezIDColumn!=nil)
-      
-      @genv.log("Creating iHOP literature search link",:info)
-      
-      ihopURLs=entrezIDs.collect do |entrezid| 
-        "http://www.ihop-net.org/UniPub/iHOP/in?dbrefs_1=NCBI_GENE__ID|#{entrezid.to_i.to_s}"
-      end
-      
-      columnIndex=ensemblColumnIndex+1
-      
-      # Insert this column after the ensembl Link (which is before other literature based stuff)
-      outputSheet.insert_column(ihopURLs,columnIndex)
-      
-      # Create the links
-      for rowi in 0...outputSheet.rows.length do
-        outputSheet.row(rowi)[columnIndex]=Spreadsheet::Link.new(url=ihopURLs[rowi],description=entrezIDs[rowi].to_i.to_s)
-      end
-      
-      # Format the links
-      outputSheet.column(columnIndex).default_format=hyperlink_format
-      
-      # And give the header a proper name
-      outputSheet.row(0)[columnIndex]="iHOP literature search"
-      
-    end
-    
-    
-    @genv.log("Formatting header",:info)
-
-    # Format the Header row
-    headerFormat=Spreadsheet::Format.new({ :weight => :bold,:size => 11 })
-    outputSheet.row(0).default_format=headerFormat
-
-    # Here we put in a little workaround for a problem with the Spreadsheet gem. 
-    # If the text "false" is in a column it will substitute nil for the false value and then fail when attempting to convert nil to an integer. 
-    # We workaround by changing the word "true" to "positive" and false to "negative"  
-    outputSheet.rows.each { |row|             
-      
-      row.each_index { |ri|         
-
-        if ( row[ri].class==NilClass)
-          p "Encountered a nil value in the sheet converting to empty string"
-          row[ri]=""
-        end
-
-        if ( row[ri]==true)
-          row[ri]="positive"
-        elsif (row[ri]==false)
-          row[ri]="negative"
-        end
-      }
-      
-
-      
-    }    
-
-
-    # Put the header rows back
-    #
-    keep_rows.reverse!
-    keep_rows.each do |row|
-      outputSheet.insert_row(0,row)      
-    end
-
-
-
-    # Finally write the results
-   @genv.log("Writing New Workbook #{outputFile}",:info)
-    outputBook.write outputFile
-  end
-
-end