Add commands to Command Palette

Author: bosborne

Diff for: BioPythonUtils.py

@@ -64,7 +64,8 @@ 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:
@@ -168,7 +169,7 @@ def run(self):
         self.result = False
 
 
-# "Download Taxon"
+# "Download Sequence by Taxon"
 class DownloadSequenceByTaxonCommand(sublime_plugin.TextCommand):
 
     def run(self, edit):
@@ -431,8 +432,8 @@ def run(self, edit):
 
                 seqin.close()
             else:
-                # Assume it's plain sequence and use an incrementing number as
-                # an id
+                # Assume it's "plain" format and use an incrementing
+                # number as an id
                 seq_id = 1
                 for seq_str in re.split('^\s*\n', seq_str, 0, re.MULTILINE):
                     seq_str = re.sub("[^a-zA-Z]", "", seq_str)

Diff for: Default (Linux).sublime-keymap

@@ -2,6 +2,7 @@
     { "keys": ["ctrl+alt+super+t"], "command": "translate" },
     { "keys": ["ctrl+alt+super+g"], "command": "genbank_to_fasta" },
     { "keys": ["ctrl+alt+super+d"], "command": "download_sequence_by_id" },
+    { "keys": ["ctrl+alt+super+s"], "command": "download_sequence_by_search" },
     { "keys": ["ctrl+alt+super+x"], "command": "download_taxon" },
     { "keys": ["ctrl+alt+super+b"], "command": "remote_blast" }
 ]

Diff for: Default (OSX).sublime-keymap

@@ -2,6 +2,7 @@
     { "keys": ["ctrl+alt+super+t"], "command": "translate" },
     { "keys": ["ctrl+alt+super+g"], "command": "genbank_to_fasta" },
     { "keys": ["ctrl+alt+super+d"], "command": "download_sequence_by_id" },
+    { "keys": ["ctrl+alt+super+s"], "command": "download_sequence_by_search" },
     { "keys": ["ctrl+alt+super+x"], "command": "download_taxon" },
     { "keys": ["ctrl+alt+super+b"], "command": "remote_blast" }
 ]

Diff for: Default (Windows).sublime-keymap

@@ -2,6 +2,7 @@
     { "keys": ["ctrl+alt+super+t"], "command": "translate" },
     { "keys": ["ctrl+alt+super+g"], "command": "genbank_to_fasta" },
     { "keys": ["ctrl+alt+super+d"], "command": "download_sequence_by_id" },
+    { "keys": ["ctrl+alt+super+s"], "command": "download_sequence_by_search" },
     { "keys": ["ctrl+alt+super+x"], "command": "download_taxon" },
     { "keys": ["ctrl+alt+super+b"], "command": "remote_blast" }
 ]

Diff for: Default.sublime-commands

@@ -24,6 +24,30 @@
         }
     },
     {
+    "caption": "BioPythonUtils: Remote Blast",
+    "command": "remote_blast"
+    },
+    {
+    "caption": "BioPythonUtils: Genbank To Fasta",
+    "command": "genbank_to_fasta"
+    },
+    {
+    "caption": "BioPythonUtils: Translate",
+    "command": "translate"
+    },
+    {
+    "caption": "BioPythonUtils: Get Sequences by Search",
+    "command": "download_sequence_by_search"
+    },
+    {
+    "caption": "BioPythonUtils: Get Sequences by Taxon",
+    "command": "download_sequence_by_taxon"
+    },
+    {
+    "caption": "BioPythonUtils: Get Sequences by Id",
+    "command": "download_sequence_by_id"
+    },
+    {
     "caption": "BioPythonUtils: Select Remote BLAST database",
     "command": "select_blast_database"
     },