bump to 0.4.50: add working ribo structure

nickp60 · Jan 27, 2018 · 579b4c4 · 579b4c4
1 parent 85c6612
commit 579b4c4
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Showing 3 changed files with 23 additions and 23 deletions.
diff --git a/riboSeed/_version.py b/riboSeed/_version.py
@@ -1 +1 @@
-__version__ = '0.4.48'
+__version__ = '0.4.50'
diff --git a/riboSeed/ribo.py b/riboSeed/ribo.py
@@ -25,19 +25,19 @@
     "Usage:   ribo <command> [options]",
     "",
     "Available commands:",
-    " -run      execute the pipeline (scan, select, seed, sketch, and score)",
-    " -scan     reannotate rRNAs in a FASTA file",
-    " -select   group rRNA annotations into rDNA operons",
-    " -seed     perform de fere novo assembly",
-    " -snag     extract rDNA regions and plot entropy",
-    " -sim      perform simulations used in manuscript",
-    " -sketch   plot results from a de fere novo assembly",
-    " -stack    compare coverage depth in rDNA regions to rest of genome",
-    " -score    score batches of assemblies with BLASTn",
-    " -swap     swap contigs from assemblies",
-    " -spec     use assembly graph to speculate number of rDNA",
-    " -struct   view the rRNA operon structure across several genomes",
-    " -config   write out a blank config file to be used with `run`",
+    " -run        execute pipeline (scan, select, seed, sketch, and score)",
+    " -scan       reannotate rRNAs in a FASTA file",
+    " -select     group rRNA annotations into rDNA operons",
+    " -seed       perform de fere novo assembly",
+    " -snag       extract rDNA regions and plot entropy",
+    " -sim        perform simulations used in manuscript",
+    " -sketch     plot results from a de fere novo assembly",
+    " -stack      compare coverage depth in rDNA regions to rest of genome",
+    " -score      score batches of assemblies with BLASTn",
+    " -swap       swap contigs from assemblies",
+    " -spec       use assembly graph to speculate number of rDNA",
+    " -structure  view the rRNA operon structure across several genomes",
+    " -config     write out a blank config file to be used with `run`",
     ""
 ]
 
@@ -69,7 +69,7 @@ def main(args=None):
         "sim": "riboSim",
         "swap": "riboSwap",
         "spec": "riboSpec",
-        "struct": "riboStructure",
+        "structure": "riboStructure",
         "config": "make_riboSeed_config"}
     if args[1] not in modules_dict.keys():
         print("Error:" + args[1] +

diff --git a/riboSeed/riboStructure.py b/riboSeed/riboStructure.py
@@ -262,15 +262,15 @@ def plot_rDNAs(
             # |                      |
             # ------------------------   0
             if "16S" in product:
-                color = mycolors['greenish']
+                color = mycolors['redish']
                 lencode = featuremin * 40
                 yjust = (2 * coding_height)/3
             elif "23S" in product:
-                color = mycolors['bluish']
+                color = mycolors['yellish']
                 lencode = featuremin * 60
                 yjust = coding_height/3
             elif "5S" in product:
-                color = mycolors['redish']
+                color = mycolors['greenish']
                 lencode = featuremin * 20
                 yjust = 0
             else:
@@ -288,13 +288,13 @@ def plot_rDNAs(
             ax.add_patch(anno_box)
             # previous_end = this_end
     # add a legend to this mess
-    red_patch = patches.Patch(color=mycolors['redish'], label='5S')
-    green_patch = patches.Patch(color=mycolors['greenish'], label='16S')
-    blue_patch = patches.Patch(color=mycolors['bluish'], label='23S')
+    red_patch = patches.Patch(color=mycolors['redish'], label='16S')
+    yellish_patch = patches.Patch(color=mycolors['yellish'], label='23S')
+    green_patch = patches.Patch(color=mycolors['greenish'], label='5S')
 
-    ax.legend(bbox_to_anchor=(.1, -0.05, .9, -.102), loc=3,
+    ax.legend(bbox_to_anchor=(.1, -0.1, .9, -.102), loc=3,
               ncol=3, mode="expand", borderaxespad=0.,
-              handles=[red_patch, green_patch, blue_patch],
+              handles=[red_patch, yellish_patch, green_patch],
               frameon=False)
     # # for righthad labels
     loc = -.1