Standardize docs and names of classes

Author: bosborne

BioPythonUtils.py

@@ -64,7 +64,7 @@ def run(self, edit):
             print("Entrez count: {}".format(ids['Count']))
             dialog_result = sublime.ok_cancel_dialog(
                 "Download {0} sequences? 'retmax': {1}".format(ids['Count'],
-                                                               entrez_retmax), 'Download')
+                    entrez_retmax), 'Download')
 
             if dialog_result is True:
                 try:
@@ -169,7 +169,7 @@ def run(self):
 
 
 # "Download Taxon"
-class DownloadTaxonCommand(sublime_plugin.TextCommand):
+class DownloadSequenceByTaxonCommand(sublime_plugin.TextCommand):
 
     def run(self, edit):
 

Main.sublime-menu

@@ -25,8 +25,8 @@
                 },
                 {
                     "id": "download_taxon",
-                    "command": "download_taxon",
-                    "caption": "Download Taxon"
+                    "command": "download_sequence_by_taxon",
+                    "caption": "Get Sequences by Taxon"
                 },
                 {
                     "id": "genbank_to_fasta",

README.md

@@ -61,8 +61,8 @@ Translation starts at the first codon and continues to the last, regardless of s
 
 #### "Get Sequences by Search"
 
-Queries [NCBI Nucleotide](https://www.ncbi.nlm.nih.gov/nucleotide/) using the [Entrez](https://www.ncbi.nlm.nih.gov/books/NBK184582/)
-search service and downloads the sequence results in GenBank format.
+Queries [NCBI Nucleotide](https://www.ncbi.nlm.nih.gov/nucleotide/) using [Entrez](https://www.ncbi.nlm.nih.gov/books/NBK184582/)
+search service and the selected text and downloads the sequence results in GenBank format.
 For example:
 ~~~~
 human[ORGN] AND AKT1[GENE]
@@ -88,7 +88,7 @@ or:
 284218, 203807
 ~~~~
 
-#### "Download Taxon"
+#### "Get Sequences by Taxon"
 
 Downloads a taxon as GenBank format entries from [NCBI](http://www.ncbi.nlm.nih.gov) using the selected
 [NCBI Taxonomy](http://www.ncbi.nlm.nih.gov/taxonomy) ids. Ids can be delimited by commas, returns, or space.