iroki 0.0.33 → 0.0.34

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: df837c589f22bbd555fb6a8afe7571524777cf14
-  data.tar.gz: 6e9dc756c45e1b2916541c0a00168dcf0be57220
+  metadata.gz: ccdbbf04cbd02148f66cc862d584cb00e54c3793
+  data.tar.gz: 30d00c03802e3925167e41c5022519b1d1e7ba49
 SHA512:
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+  data.tar.gz: 0f44b3a502cfeb5c59703dedf384813128992bdf1589f7afe59568fbcb1193472a3285f5641ab6f9bcb0807801138c7913872f87922f75d9364719e82db85b9f

data/lib/iroki/main/main.rb

@@ -252,6 +252,10 @@ module Iroki
                name_map_f.nil?,
                "Newick file was given but no other files were given")
 
+      abort_if biom_f && !exact,
+               "Regex matching cannot be used with a biom file. " +
+               "Pass the --exact flag"
+
       # treeio = Bio::FlatFile.open(Bio::Newick, newick)
 
       # newick = treeio.next_entry
@@ -285,11 +289,11 @@ module Iroki
       #################################################################
       # get color patterns
       ####################
-      if color_map_f && biom_f
-        color_map_patterns = parse_color_map_iroki color_map_f,
-                                                   iroki_to_name,
-                                                   exact_matching: exact,
-                                                   auto_color: auto_color_hash
+      if biom_f
+        abort_if single_color,
+                 "--single-color is not compatible with a two " +
+                 "group biom file. Please remove that option."
+
         samples, counts, is_single_group = Biom.open(biom_f, "rt").parse
 
         if is_single_group
@@ -299,6 +303,9 @@ module Iroki
                                                   min_lumin,
                                                   max_lumin).patterns
         else
+          # abort_if single_color,
+          #          "--single-color is incompatible with a two group biom file, please remove it."
+
           g1_counts = counts.map(&:first)
           g2_counts = counts.map(&:last)
           biom_patterns = TwoGroupGradient.new(samples,
@@ -307,6 +314,13 @@ module Iroki
                                                min_lumin,
                                                max_lumin).patterns
         end
+      end
+
+      if color_map_f && biom_f
+        color_map_patterns = parse_color_map_iroki color_map_f,
+                                                   iroki_to_name,
+                                                   exact_matching: exact,
+                                                   auto_color: auto_color_hash
 
         # these patterns have the original name for the key, so change
         # the key to the iroki name
@@ -337,23 +351,7 @@ module Iroki
                                          exact_matching: exact,
                                          auto_color: auto_color_hash
       elsif biom_f
-        samples, counts, is_single_group = Biom.open(biom_f, "rt").parse
-
-        if is_single_group
-          patterns = SingleGroupGradient.new(samples,
-                                             counts,
-                                             single_color,
-                                             min_lumin,
-                                             max_lumin).patterns
-        else
-          g1_counts = counts.map(&:first)
-          g2_counts = counts.map(&:last)
-          patterns = TwoGroupGradient.new(samples,
-                                          g1_counts,
-                                          g2_counts,
-                                          min_lumin,
-                                          max_lumin).patterns
-        end
+        patterns = biom_patterns
 
         # these patterns have the original name for the key, so change
         # the key to the iroki name

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.33"
+  VERSION = "0.0.34"
   COPYRIGHT = "2015 - 2017 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: 0.0.33
+  version: 0.0.34
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-04-28 00:00:00.000000000 Z
+date: 2017-05-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler