Add utility scripts

Author: mooreryan

bin/biom_convert

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+infile="$1"
+
+biom convert -i "$infile" -o "$infile".tsv --to-tsv
+
+awk 'BEGIN { FS="\t"; OFS="\t" }
+{
+  if (NR == 2)
+  {
+    $1 = "name";
+    print;
+  }
+  else if (NR >= 3)
+  {
+    print;
+  }
+}' "$infile".tsv > "$infile".tsv.iroki.txt

bin/biom_tsv_to_iroki

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+infile="$1"
+
+awk 'BEGIN { FS="\t"; OFS="\t" }
+{
+  if (NR == 2)
+  {
+    $1 = "name";
+    print;
+  }
+  else if (NR >= 3)
+  {
+    print;
+  }
+}' "$infile"

bin/combine_biom_files.rb

@@ -0,0 +1,100 @@
+#!/usr/bin/env ruby
+
+Signal.trap("PIPE", "EXIT")
+
+require "abort_if"
+
+include AbortIf
+
+require "trollop"
+
+opts = Trollop.options do
+  banner <<-EOS
+
+  Combine multiple biom files, e.g., the output from running
+  multiple_rarefactions.py.
+
+  Weird things may happen like not every biom file has every OTU or
+  not every biom file has every sample (due to the rarefaction), but
+  this will just count up everything.
+
+  Options:
+  EOS
+
+  opt(:biom, "Biom files", type: :strings)
+  opt(:method, "Method to combine values", default: "mean")
+end
+
+VALID_METHODS = %w[mean]
+
+abort_if !opts[:biom] || opts[:biom].empty?,
+         "--biom is a required option"
+
+opts[:biom].each do |fname|
+  abort_unless_file_exists fname
+end
+
+abort_unless VALID_METHODS.include?(opts[:method]),
+             "--method must be one of #{VALID_METHODS.join(', ')}.  Got: #{opts[:method]}"
+
+num_biom_files = opts[:biom].count
+all_samples = []
+otus = {}
+
+opts[:biom].each do |fname|
+
+  cidx2sample = {}
+
+  idx = 0
+  File.open(fname, "rt").each_line do |line|
+    line.chomp!
+    unless line == "# Constructed from biom file"
+      ary = line.split "\t"
+
+      this_otu = nil
+
+      if idx.zero?
+        ary.each_with_index do |sample, cidx|
+          # the first one should be name
+          unless cidx == 0
+            all_samples << sample
+            cidx2sample[cidx] = sample
+          end
+        end
+      else
+        ary.each_with_index do |item, cidx|
+          # these are the data rows
+          if cidx == 0
+            this_otu = item
+
+            unless otus.has_key? this_otu
+              otus[this_otu] = Hash.new 0
+            end
+          else
+            count = item
+            sample = cidx2sample[cidx]
+            otus[this_otu][sample] += count.to_f
+          end
+        end
+      end
+
+      idx += 1
+    end
+  end
+end
+
+all_samples.uniq!
+
+puts ["name", all_samples].join "\t"
+
+otus.each do |otu, counts|
+  count_str = all_samples.map do |sample|
+    if opts[:method] == "mean"
+      counts[sample] / num_biom_files.to_f
+    else
+      counts[sample]
+    end
+  end.join "\t"
+
+  puts [otu, count_str].join "\t"
+end

bin/log_transform

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+awk 'BEGIN {FS="\t"; OFS="\t"}
+{
+  if (NR == 1) {
+    print;
+  }
+  else {
+    for (i = 2; i <= NF; ++i) {
+      if ($i <= 1) {
+        $i = 0;
+      }
+      else {
+        $i = log($i);
+      }
+    }
+    {
+      print;
+    }
+  }
+}' "$1" > "${1%.*}".log_transform.txt