iroki 0.0.19 → 0.0.20

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -160,3 +160,7 @@ Add `reorder_nodes` script.
 ### 0.0.19 ###
 
 - Remove assertion that color map cannot have entries that aren't in the newick file
+
+### 0.0.20 ###
+
+- Handle more examples of bad biom files and bad name maps

data/lib/iroki/biom.rb

@@ -16,6 +16,10 @@
 # You should have received a copy of the GNU General Public License
 # along with Iroki.  If not, see <http://www.gnu.org/licenses/>.
 
+def count_or_rel_abund? str
+  str.match /\A[01]?.?[0-9]+\Z/
+end
+
 module Iroki
   class Biom < File
     attr_accessor :single_group
@@ -31,12 +35,24 @@ module Iroki
           lineno += 1
           sample, *the_counts = line.chomp.split "\t"
 
+          abort_if sample.nil? || sample.empty? || sample =~ / +/,
+                   "Line #{idx+1} has no sample"
+
+          the_counts.flatten.each do |count|
+            abort_unless count_or_rel_abund?(count),
+                         "The value '#{count}' in the biom file " +
+                         "was not a count or relative abundance"
+          end
+
           if lineno.zero?
             first_line_count = the_counts.count
           else
             abort_unless first_line_count == the_counts.count,
-                         "The biom file has rows with different " +
-                         "numbers of columns"
+                         "Line number #{idx+1} (#{line.inspect}) in the " +
+                         "biom file has #{the_counts.count} " +
+                         "columns when it should have " +
+                         "#{first_line_count} columns like the " +
+                         "first row does."
           end
 
           samples << sample

data/lib/iroki/core_ext/file/file.rb

@@ -226,6 +226,9 @@ module Iroki
         name_map = {}
         Object::File.open(fname, "rt").each_line do |line|
           unless line.start_with? "#"
+            abort_if line.chomp.split("\t").count > 2,
+                     "Line (#{line.inspect}) has more than two columns"
+
             oldname, newname = line.chomp.split "\t"
 
 

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.19"
+  VERSION = "0.0.20"
   COPYRIGHT = "2015 - 2016 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/iroki"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: iroki
 version: !ruby/object:Gem::Version
-  version: 0.0.19
+  version: 0.0.20
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-08-17 00:00:00.000000000 Z
+date: 2016-08-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler