bio-table 0.0.2 → 0.0.3

data/README.md

@@ -2,14 +2,14 @@
 
 [![Build Status](https://secure.travis-ci.org/pjotrp/bioruby-table.png)](http://travis-ci.org/pjotrp/bioruby-table)
 
-bio-table is the swiss knife of tabular data.
-Tables of data are often used in bioinformatics, especially in
-conjunction with Excel spreadsheets and DB queries. This biogem
-contains support for reading tables, writing tables, and manipulation
-of rows and columns, both using a command line interface and through a
-Ruby library. If you don't like R dataframes, maybe you like this.
-Also, because bio-table is command line driven, it easily fits in a
-pipe-line setup. 
+bio-table is the swiss knife of tabular data.  Tables of data are
+often used in bioinformatics, especially in conjunction with Excel
+spreadsheets and DB queries. This biogem contains support for reading
+tables, writing tables, and manipulation of rows and columns, both
+using a command line interface and through a Ruby library. If you
+don't like R dataframes, maybe you like this.  Also, because bio-table
+is command line driven, and can use STDIN and STDOUT, it easily fits
+in a pipe-line setup. 
 
 Quick example, say we want to filter out rows that contain certain
 p-values listed in the 4th column:
@@ -18,11 +18,24 @@ p-values listed in the 4th column:
     bio-table test/data/input/table1.csv --num-filter "values[3] <= 0.05"
 ```
 
-bio-table should be lazy, be good for big data, and the library
-support a functional style of programming. You don't need to know Ruby
-to use the command line interface (CLI).
+bio-table should be lazy. And be good for big data, bio-table is
+designed so that most important functions do not load the data in
+memory. The library supports a functional style of programming, but
+you don't need to know Ruby to use the command line interface (CLI).
 
-Note: this software is under active development!
+Features:
+
+* Support for TAB and CSV files
+* Filter on data
+* Transform table and data by column
+* Recalculate data
+* Diff between tables, selecting on specific column values
+* Merge tables side by side
+* Split tables by column
+* Read from STDIN, write to STDOUT
+
+Note: this software is under active development, though it should just
+work.
 
 ## Installation
 
@@ -100,12 +113,13 @@ To reorder/reduce table columns by name
     bio-table test/data/input/table1.csv --columns AJ,B6,Axb1,Axb4,AXB13,Axb15,Axb19 > test1a.tab
 ```
 
-or use their index numbers
+or use their index numbers (the first column is zero)
 
 ```
     bio-table test/data/input/table1.csv --columns 0,1,8,2,4,6 > test1a.tab
 ```
 
+
 To filter for columns using a regular expression
 
 ```
@@ -169,7 +183,10 @@ with rownames that appear in table2, but not in table1)
 
     bio-table --diff 0 table1.csv table2.csv 
 
-To find it the other way, switch the file names
+bio-table --diff is different from the standard Unix diff tool. The
+latter shows insertions and deletions. bio-table --diff shows what is
+in one file, and not in the other (insertions). To see deletions,
+reverse the file order, i.e. switch the file names
 
     bio-table --diff 0 table1.csv table2.csv 
 
@@ -177,19 +194,32 @@ To diff on something else
 
     bio-table --diff 0,3 table2.csv table1.csv 
 
-creates a (hopefully unique) key using columns 0 and 3 (0 is the rownames column).
+creates a key using columns 0 and 3 (0 is the rownames column).
 
 Similarly
 
     bio-table --overlap 2 table1.csv table2.csv
 
-finds the overlapping rows, based on column 2 (NYI)
+finds the overlapping rows, based on the content of column 2.
+
 
 ### Different parsers
 
 more soon
 
-## Usage
+### Using STDIN
+
+bio-table can read data from STDIN, by simply assuming that the data
+piped in is the first input file
+
+```
+    cat test1.tab | bio-table table1.csv --num-filter "values[3] <= 0.05" > test1a.tab
+```
+
+will filter both files test1.tab and test1.csv and output to
+test1a.tab.
+
+## bio-table API (for Ruby programming)
 
 ```ruby
     require 'bio-table'

data/Rakefile

@@ -17,7 +17,7 @@ Jeweler::Tasks.new do |gem|
   gem.name = "bio-table"
   gem.homepage = "http://github.com/pjotrp/bioruby-table"
   gem.license = "MIT"
-  gem.summary = %Q{Swiss knife of tabulated data; transforming/filtering tab/csv files}
+  gem.summary = %Q{Swiss army knife of tabulated data; transforming/filtering tab/csv files}
   gem.description = %Q{Functions and tools for tranforming and changing tab delimited and comma separated table files - useful for Excel sheets and SQL/RDF output}
   gem.email = "pjotr.public01@thebird.nl"
   gem.authors = ["Pjotr Prins"]

data/VERSION

@@ -1 +1 @@
-0.0.2
+0.0.3

data/bin/bio-table

@@ -9,6 +9,8 @@ $: << File.join(rootpath,'lib')
 
 _VERSION = File.new(File.join(rootpath,'VERSION')).read.chomp
 
+INPUT_ON_STDIN = !$stdin.tty?
+
 $stderr.print "bio-table "+_VERSION+" Copyright (C) 2012 Pjotr Prins <pjotr.prins@thebird.nl>\n\n"
 
 USAGE =<<EOU
@@ -17,7 +19,7 @@ bio-table transforms, filters and reorders table files (CSV, tab-delimited).
 
 EOU
 
-if ARGV.size == 0
+if ARGV.size == 0 and not INPUT_ON_STDIN
   print USAGE
 end
 
@@ -32,7 +34,7 @@ Bio::Log::CLI.logger('stderr')
 Bio::Log::CLI.trace('info')
 
 options = {show_help: false, write_header: true}
-options[:show_help] = true if ARGV.size == 0
+options[:show_help] = true if ARGV.size == 0 and not INPUT_ON_STDIN
 opts = OptionParser.new do |o|
   o.banner = "Usage: #{File.basename($0)} [options] filename\n\n"
 
@@ -73,6 +75,10 @@ opts = OptionParser.new do |o|
   end
 
   o.on('--overlap list',Array,'Find overlap of two input files on columns)') do |l|
+    if l.size==1 and File.exist?(l.first)
+      ARGV.unshift l.first
+      l = ["0"]
+    end
     options[:overlap] = l
   end
   
@@ -146,6 +152,11 @@ end
 
 if options[:overlap]
   logger.warn "Column settings are ignored for --overlap" if options[:columns]
+  logger.warn "Ignoring extraneaous files "+ARGV[2..-1].join(",") if ARGV.size>2
+  t1 = TableReader::read_file(ARGV[0], options)
+  t2 = TableReader::read_file(ARGV[1], options)
+  t = Overlap::overlap_tables(t1,t2, options)
+  t.write(options)
   exit
 end
 
@@ -159,8 +170,32 @@ if options[:merge]
   exit
 end
 
+#
+# We also support STDIN for the first 'file'. A non-blocking idea can
+# be found here:
+#
+# http://eric.lubow.org/2010/ruby/multiple-input-locations-from-bash-into-ruby/
+#
+
+writer = BioTable::TableWriter::Writer.new(options[:format])
+
+if INPUT_ON_STDIN
+  opts = options.dup # so we can modify options
+  BioTable::TableLoader.emit(STDIN, opts).each do |row| 
+    writer.write(TableRow.new(row[0],row[1..-1]))
+  end
+  options[:write_header] = false  # don't write the header for chained files
+end
+
 ARGV.each do | fn |
-  t = TableReader::read_file(fn, options)
-  t.write(options)
+  opts = options.dup # so we can modify options
+  f = File.open(fn,"r")
+  if not opts[:in_format] and fn =~ /\.csv$/
+    logger.debug "Autodetected CSV file"
+    opts[:in_format] = :csv
+  end
+  BioTable::TableLoader.emit(f, opts).each do |row| 
+    writer.write(TableRow.new(row[0],row[1..-1]))
+  end
   options[:write_header] = false  # don't write the header for chained files
 end

data/features/iterate_table.feature

@@ -0,0 +1,16 @@
+Feature: Iterate through an input table
+
+  bio-table should read input line by line as an iterator, and emit
+  filtered/transformed output
+
+  Scenario: Iterate through a table
+    Given I want to iterate a comma separated table
+        """
+        #Gene,AJ,B6,Axb1,Axb2,Axb4,Axb12,AXB13,Axb15,Axb19,Axb23,Axb24,Bxa1,Bxa2,Bxa4,Bxa7,Bxa8,Bxa12,Bxa11,Bxa13,Bxa15,Bxa16,Axb5,Axb6,Axb8,Axb1,Bxa24,Bxa25,Bxa26,gene_symbol,gene_desc
+        105853,0.06,0,0,0,0,0,0.11,0,0,0,,,0,0,0,0,0,0,0,0,0,0,0,0,,0,,,Mal2,"MAL2 proteolipid protein"
+        105855,236.88,213.95,213.15,253.49,198,231.56,200.96,255.2,214.04,231.46,,,233.23,241.26,237.53,171.87,237.13,162.3,252.13,284.85,188.76,253.43,220.15,305.52,,217.42,,,Nckap1l,"NCK associated protein 1 like,NCK associated protein 1 like,"
+        105859,0,0.14,0,0,0.07,0.04,0,0,0,0,,,0.02,0,0,0,0,0,0.06,0,0,0,0.02,0,,0,,,Csdc2,"RNA-binding protein pippin"
+        105866,0,0,0,0,0,0,0,0,0,0,,,0,0,0,0,0,0,0,0,0,0,0,0,,0,,,Krt72,"keratin 72"
+        """
+    When I iterate through the table
+

data/features/step_definitions/iterate_table.rb

@@ -0,0 +1,11 @@
+Given /^I want to iterate a comma separated table$/ do |string|
+  @lines = string.split(/\n/).map { |s| s.strip }
+end
+
+When /^I iterate through the table$/ do
+  res = []
+  BioTable::TableLoader.emit(@lines, :in_format => :csv).each { |row| res << row }
+  res[3][5].should == "0.07"
+end
+
+

data/lib/bio-table.rb

@@ -18,8 +18,10 @@ require 'bio-table/parser.rb'
 require 'bio-table/formatter.rb'
 require 'bio-table/tablerow.rb'
 require 'bio-table/table.rb'
+require 'bio-table/tableload.rb'
 require 'bio-table/tablereader.rb'
 require 'bio-table/tablewriter.rb'
+require 'bio-table/table_apply.rb'
 require 'bio-table/diff.rb'
 require 'bio-table/overlap.rb'
 require 'bio-table/merge.rb'

data/lib/bio-table/filter.rb

@@ -1,5 +1,20 @@
 module BioTable
 
+  class LazyValues
+    def initialize fields
+      @fields = fields
+      @values = []  # cache values
+    end
+
+    def [] index
+      if not @values[index]
+        field = @fields[index]
+        @values[index] = (Filter::valid_number?(field) ? field.to_f : nil )
+      end
+      @values[index]
+    end
+  end
+
   module Filter
 
     # Create an index to the column headers, so header A,B,C,D with columns
@@ -54,7 +69,8 @@ module BioTable
     def Filter::numeric code, fields
       return true if code == nil
       if fields
-        values = fields.map { |field| (valid_number?(field) ? field.to_f : nil ) } # FIXME: not so lazy
+        # values = fields.map { |field| (valid_number?(field) ? field.to_f : nil ) } # FIXME: not so lazy
+        values = LazyValues.new(fields)
         begin
           eval(code)
         rescue Exception

data/lib/bio-table/overlap.rb

@@ -1 +1,26 @@
 # Overlap module
+#
+module BioTable
+
+  module Overlap
+
+    def self.overlap_tables t1, t2, options 
+      logger = Bio::Log::LoggerPlus['bio-table']
+      columns = Columns::to_list(options[:overlap])
+      t = Table.new(t1.header)
+      l1 = t1.map { |row| columns.map { |i| row.all_fields[i] } }
+      l2 = t2.map { |row| columns.map { |i| row.all_fields[i] } }
+      logger.warn "Not all selected keys are unique!" if l1.uniq.size != l1.size or l2.uniq.size != l2.size
+      overlap = l2 & l1
+      # p overlap
+      # create index for table 2
+      idx2 = Indexer::create_index(t2,columns)
+      overlap.each do |values|
+        t.push(t2.row_by_columns(columns.zip(values),idx2))
+      end
+      t
+    end
+
+  end
+
+end

data/lib/bio-table/table.rb

@@ -1,5 +1,7 @@
 module BioTable
 
+  # In memory table representation - note that the default parser/emitter does not
+  # use this class as it expects all data to be in memory.
   class Table
 
     include Enumerable
@@ -19,45 +21,27 @@ module BioTable
       @name = File.basename(fn,File.extname(fn))
     end
 
-    # Read lines (list of string) and add them to the table, setting row names 
-    # and row fields. The first row is assumed to be the header and ignored if the
-    # header has been set.
+    # Read lines (list/array of string) and add them to the table, setting row
+    # names and row fields. The first row is assumed to be the header and
+    # ignored if the header has been set.
 
     def read_lines lines, options = {}
-      # get all the options
-      num_filter  = options[:num_filter]
-      @logger.debug "Filtering on #{num_filter}" if num_filter 
-      rewrite  = options[:rewrite]
-      @logger.debug "Rewrite #{rewrite}" if rewrite
-      use_columns = options[:columns]
-      @logger.debug "Filtering on columns #{use_columns}" if use_columns 
-      column_filter = options[:column_filter]
-      @logger.debug "Filtering on column names #{column_filter}" if column_filter
-      include_rownames = options[:with_rownames]
-      @logger.debug "Include row names" if include_rownames
-      first_column = (include_rownames ? 0 : 1)
-
-      # parse the header
-      header = LineParser::parse(lines[0], options[:in_format])
-      Validator::valid_header?(header, @header)
-      @header = header if not @header
+      table_apply = TableApply.new(options)
 
-      column_index = Filter::create_column_index(use_columns,header)
-      column_index = Filter::filter_column_index(column_index,header,column_filter)
-      @header = Filter::apply_column_filter(header,column_index)
+      header = table_apply.parse_header(lines[0], options)
+      Validator::valid_header?(header, @header)  # compare against older header when merging
+      column_index,header = table_apply.column_index(header) # we may rewrite the header
+      @header = header if not @header
 
       # parse the rest
-      (lines[1..-1]).each do | line |
-        fields = LineParser::parse(line, options[:in_format])
-        fields = Filter::apply_column_filter(fields,column_index) 
-        rowname = fields[0]
-        data_fields = fields[first_column..-1]
-        next if not Validator::valid_row?(data_fields,@header,@rows)
-        next if not Filter::numeric(num_filter,data_fields)
-        (rowname, data_fields) = Rewrite::rewrite(rewrite,rowname,data_fields)
-
-        @rownames << rowname if not include_rownames # otherwise doubles rownames
-        @rows << data_fields
+      prev_line = @header[1..-1]
+      (lines[1..-1]).each_with_index do | line, line_num |
+        rowname, data_fields = table_apply.parse_row(line_num, line, column_index, prev_line, options)
+        if data_fields
+          @rownames << rowname if not options[:with_rownames] # otherwise doubles rownames
+          @rows << data_fields if data_fields
+        end
+        prev_line = data_fields
       end
     end
 
@@ -82,7 +66,7 @@ module BioTable
       formatter.write(@header) if options[:write_header]
       each do | tablerow |
         # p tablerow
-        formatter.write(tablerow.all_fields) if tablerow.valid?
+        formatter.write(tablerow.all_fields) if tablerow.all_valid?
       end
     end
 

data/lib/bio-table/table_apply.rb

@@ -0,0 +1,49 @@
+module BioTable
+
+  # Apply filters/rewrite etc. to a table, visiting a row at a time. For optimization
+  # this class contains some state
+  class TableApply
+
+    def initialize options
+      @logger = Bio::Log::LoggerPlus['bio-table']
+
+      @num_filter  = options[:num_filter]
+      @logger.debug "Filtering on #{@num_filter}" if @num_filter 
+      @rewrite  = options[:rewrite]
+      @logger.debug "Rewrite #{@rewrite}" if @rewrite
+      @use_columns = options[:columns]
+      @logger.debug "Filtering on columns #{@use_columns}" if @use_columns 
+      @column_filter = options[:column_filter]
+      @logger.debug "Filtering on column names #{@column_filter}" if @column_filter
+      @include_rownames = options[:with_rownames]
+      @logger.debug "Include row names" if @include_rownames
+      @first_column = (@include_rownames ? 0 : 1)
+    end
+
+    def parse_header(line, options)  
+      LineParser::parse(line, options[:in_format])
+    end
+
+    def column_index(header)
+      column_idx = Filter::create_column_index(@use_columns,header)
+      column_idx = Filter::filter_column_index(column_idx,header,@column_filter)
+      new_header = Filter::apply_column_filter(header,column_idx)
+      return column_idx, new_header
+    end
+
+    def parse_row(line_num, line, column_idx, last_fields, options)
+      fields = LineParser::parse(line, options[:in_format])
+      fields = Filter::apply_column_filter(fields,column_idx) 
+      return nil,nil if fields == []
+      rowname = fields[0]
+      data_fields = fields[@first_column..-1]
+      if data_fields.size > 0
+        return nil,nil if not Validator::valid_row?(line_num, data_fields, last_fields)
+        return nil,nil if not Filter::numeric(@num_filter,data_fields)
+        (rowname, data_fields) = Rewrite::rewrite(@rewrite,rowname,data_fields)
+      end
+      return rowname, data_fields
+    end
+  end
+
+end

data/lib/bio-table/tableload.rb

@@ -0,0 +1,39 @@
+module BioTable
+
+  module TableLoader
+
+    # Emit a row at a time, using generator as input (the generator should have
+    # an 'each' method) and apply the filters etc. defined in options
+    #
+    # Note that this class does not hold data in memory(!)
+    #
+    # Note that you need to pass in :with_header to get the header row
+    def TableLoader::emit generator, options 
+      table_apply = TableApply.new(options)
+      column_index = nil, prev_line = nil
+      Enumerator.new { |yielder|
+        # fields = LineParser::parse(line,options[:in_format])
+        generator.each_with_index do |line, line_num|
+          # p [line_num, line]
+          if line_num == 0
+            header = table_apply.parse_header(line, options)
+            # Validator::valid_header?(header, @header)  # compare against older header when merging
+            column_index,header = table_apply.column_index(header) # we may rewrite the header
+            yielder.yield header if options[:write_header] != false
+            prev_line = header[1..-1]
+          else
+            rowname, data_fields = table_apply.parse_row(line_num, line, column_index, prev_line, options)
+            if data_fields
+              list = []
+              list << rowname if not options[:with_rownames] # otherwise doubles rownames
+              list += data_fields if data_fields
+              yielder.yield list
+              prev_line = data_fields
+            end
+          end
+        end
+      }
+    end
+
+  end
+end

data/lib/bio-table/tablerow.rb

@@ -1,5 +1,6 @@
 module BioTable
 
+  # Abstraction of a parsed table row
   class TableRow
     attr_reader :rowname, :fields
     def initialize rowname, fields = []
@@ -15,6 +16,10 @@ module BioTable
       ([@rowname] << @fields).flatten
     end
 
+    def all_valid?
+      all_fields != nil and all_fields.size > 0
+    end
+  
     def valid?
       fields != nil and fields.size > 0
     end

data/lib/bio-table/tablewriter.rb

@@ -1,6 +1,16 @@
 module BioTable
 
   module TableWriter
+
+    class Writer
+      def initialize format=:tab
+        @formatter = FormatFactory::create(format)
+      end
+
+      def write row
+        @formatter.write(row.all_fields) if row.all_valid?
+      end
+    end
   end
 
 end

data/lib/bio-table/validator.rb

@@ -12,12 +12,12 @@ module BioTable
       true
     end
 
-    def Validator::valid_row? fields, header, rows
+    def Validator::valid_row? line_number, fields, last_fields
       return false if fields == nil or fields.size == 0
-      if rows.size>0 and (fields.size != rows.last.size)
-        p rows.last
+      if last_fields.size>0 and (fields.size != last_fields.size)
+        p last_fields
         p fields
-        throw "Number of fields diverge in line #{rows.size + 1} (size #{fields.size}, expected #{rows.last.size})"
+        throw "Number of fields diverge in line #{line_number} (size #{fields.size}, expected #{last_fields.size})"
       end
       true
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-table
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-15 00:00:00.000000000Z
+date: 2012-07-26 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &23495840 !ruby/object:Gem::Requirement
+  requirement: &27789060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *23495840
+  version_requirements: *27789060
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &23495320 !ruby/object:Gem::Requirement
+  requirement: &27788560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 2.8.0
   type: :development
   prerelease: false
-  version_requirements: *23495320
+  version_requirements: *27788560
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &23494780 !ruby/object:Gem::Requirement
+  requirement: &27788060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *23494780
+  version_requirements: *27788060
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &23494180 !ruby/object:Gem::Requirement
+  requirement: &27787540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *23494180
+  version_requirements: *27787540
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &23493680 !ruby/object:Gem::Requirement
+  requirement: &27787060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -65,10 +65,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *23493680
+  version_requirements: *27787060
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &23493160 !ruby/object:Gem::Requirement
+  requirement: &25379120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +76,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *23493160
+  version_requirements: *25379120
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &23492660 !ruby/object:Gem::Requirement
+  requirement: &25378640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *23492660
+  version_requirements: *25378640
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &23492180 !ruby/object:Gem::Requirement
+  requirement: &25378160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -98,7 +98,7 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *23492180
+  version_requirements: *25378160
 description: Functions and tools for tranforming and changing tab delimited and comma
   separated table files - useful for Excel sheets and SQL/RDF output
 email: pjotr.public01@thebird.nl
@@ -118,9 +118,11 @@ files:
 - Rakefile
 - VERSION
 - bin/bio-table
-- features/bio-table-csv-reader-feature.rb
 - features/bio-table-csv-reader.feature
+- features/iterate_table.feature
+- features/step_definitions/bio-table-csv-reader-feature.rb
 - features/step_definitions/bio-table_steps.rb
+- features/step_definitions/iterate_table.rb
 - features/support/env.rb
 - lib/bio-table.rb
 - lib/bio-table/columns.rb
@@ -133,6 +135,8 @@ files:
 - lib/bio-table/parser.rb
 - lib/bio-table/rewrite.rb
 - lib/bio-table/table.rb
+- lib/bio-table/table_apply.rb
+- lib/bio-table/tableload.rb
 - lib/bio-table/tablereader.rb
 - lib/bio-table/tablerow.rb
 - lib/bio-table/tablewriter.rb
@@ -156,7 +160,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1776127102043822175
+      hash: -1964296020152295186
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -168,5 +172,5 @@ rubyforge_project:
 rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
-summary: Swiss knife of tabulated data; transforming/filtering tab/csv files
+summary: Swiss army knife of tabulated data; transforming/filtering tab/csv files
 test_files: []