Handle different databases for the different BLAST applications

bosborne · Feb 19, 2017 · 621a17e · 621a17e
1 parent 1e6ee72
commit 621a17e
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Showing 6 changed files with 134 additions and 118 deletions.
diff --git a/BioPythonUtils.py b/BioPythonUtils.py
@@ -6,6 +6,7 @@
 import time
 import sys
 import os
+import json
 # BioPython 1.68 is bundled with this package
 sys.path.append(os.path.dirname(__file__))
 from Bio import SeqIO, Entrez
@@ -14,13 +15,15 @@
 from Bio.Alphabet import IUPAC
 from Bio.Blast import NCBIWWW
 
-# Use globals which can be set by show_quick_panel()
+# Get BLAST details from the JSON config file
+app_info = json.load(open(os.path.join(os.path.dirname(__file__),
+                                       "config.json")))
+blast_formats = app_info['blast_formats']
+blast_info = app_info['blast_info']
+# Globals which are used or set by show_quick_panel()
 blast_db = None
 blast_app = None
 blast_format = None
-blast_apps = ['blastp', 'blastn', 'blastx', 'tblastn', 'tblastx']
-blast_formats = ['HTML', 'Text', 'ASN.1', 'XML']
-blast_dbs = ['nr', 'refseq', 'swissprot', 'pat', 'month', 'pdb', 'env_nr']
 
 
 # "Download Sequence by Search"
@@ -31,10 +34,6 @@ def run(self, edit):
         entrez_retmax = sublime.load_settings(
             'BioPythonUtils.sublime-settings').get('entrez_retmax')
 
-        # Default is 20
-        if not entrez_retmax:
-            entrez_retmax = 20
-
         email_for_eutils = sublime.load_settings(
             'BioPythonUtils.sublime-settings').get('email_for_eutils')
 
@@ -403,14 +402,6 @@ def run(self, edit):
             sublime.error_message("No BLAST database specified")
             return
 
-        if not blast_app:
-            sublime.error_message("No BLAST application specified")
-            return
-
-        if not blast_format:
-            sublime.error_message("No BLAST format specified")
-            return
-
         # 1 page is written for each report if there are multiple selections
         for region in self.view.sel():
             seq_str = self.view.substr(region)
@@ -451,43 +442,41 @@ def run(self, edit):
 class SelectBlastDatabase(sublime_plugin.WindowCommand):
 
     def run(self):
-        global blast_dbs
-        sublime.active_window().show_quick_panel(blast_dbs, setBlastDatabase)
+        sublime.active_window().show_quick_panel(
+            blast_info[blast_app], setBlastDatabase)
+
+
+def setBlastDatabase(index):
+    global blast_db
+    if index > -1:
+        blast_db = blast_info[blast_app][index]
 
 
 class SelectBlastApplication(sublime_plugin.WindowCommand):
 
     def run(self):
-        global blast_apps
         sublime.active_window().show_quick_panel(
-            blast_apps, setBlastApplication)
+            list(blast_info.keys()), setBlastApplication)
+
+
+def setBlastApplication(index):
+    global blast_app
+    if index > -1:
+        blast_app = list(blast_info.keys())[index]
 
 
 class SelectBlastFormat(sublime_plugin.WindowCommand):
 
     def run(self):
-        global blast_formats
         sublime.active_window().show_quick_panel(blast_formats, setBlastFormat)
 
 
 def setBlastFormat(index):
-    global blast_format, blast_formats
+    global blast_format
     if index > -1:
         blast_format = blast_formats[index]
 
 
-def setBlastDatabase(index):
-    global blast_db, blast_dbs
-    if index > -1:
-        blast_db = blast_dbs[index]
-
-
-def setBlastApplication(index):
-    global blast_app, blast_apps
-    if index > -1:
-        blast_app = blast_apps[index]
-
-
 def validate_nt(seq):
     # Valid: {'G', 'T', 'U', 'C', 'A'}
     valid_bases = set(IUPAC.unambiguous_dna.letters +

diff --git a/BioPythonUtils.sublime-settings b/BioPythonUtils.sublime-settings
@@ -1,7 +1,7 @@
 {
-    "email_for_eutils": "",    // This email address will be used for EUtils queries
-    "entrez_retmax": "",       // Maximum number of Entrez records downloaded
-    "remote_blast_app": "",    // blastp, blastn, blastx, tblastn, tblastx
-    "remote_blast_format": "", // HTML, Text, ASN.1, XML
-    "remote_blast_db": ""      // nr, refseq, swissprot, pat, month, pdb, env_nr
+    "email_for_eutils": "",        // This email address will be used for EUtils queries
+    "entrez_retmax": "1000",       // Maximum number of Entrez records downloaded
+    "remote_blast_app": "blastp",  // blastp, blastn, blastx, tblastn, tblastx
+    "remote_blast_format": "Text", // HTML, Text, ASN.1, XML
+    "remote_blast_db": "nr"        // Will depend on the BLAST application
 }
diff --git a/README.md b/README.md
@@ -95,8 +95,7 @@ Downloads a taxon as GenBank format entries from [NCBI](http://www.ncbi.nlm.nih.
 
 #### "Remote BLAST"
 
-Sends the selected Fasta format or "plain" sequence(s) to the [BLAST server at NCBI](http://blast.ncbi.nlm.nih.gov/Blast.cgi) and retrieves the results. Set the application, database, and result format using the Command Palette. You can also set default values
-for these in your "Settings - User" file ("remote_blast_app", "remote_blast_db", "remote_blast_format").
+Sends the selected Fasta format or "plain" sequence(s) to the [BLAST server at NCBI](http://blast.ncbi.nlm.nih.gov/Blast.cgi) and retrieves the results. You can set the application, database, and result format using the Command Palette. You can also set some default values in your "Settings - User" file ("remote_blast_app", "remote_blast_format"). Note that the available databases changes depending on the BLAST application.
 
 #### "Genbank To Fasta"
 

diff --git a/config.json b/config.json
@@ -1,79 +1,87 @@
 {
-  "blastn": [
-    "alu_repeats",
-    "Bacteria and Archaea",
-    "chromosome",
-    "dbsts",
-    "est",
-    "gss",
-    "HTGS",
-    "nr/nt",
-    "pat",
-    "pdb",
-    "refseq_gene",
-    "refseq_genomic",
-    "refseq_representative_genomes",
-    "refseq_rna",
-    "SRA",
-    "TSA",
-    "wgs"
+  "blast_formats": [
+    "HTML",
+    "Text",
+    "ASN.1",
+    "XML"
   ],
-  "blastp": [
-    "env_nr",
-    "landmark"
-    "nr",
-    "pat",
-    "pdb",
-    "refseq_protein",
-    "swissprot",
-    "tsa_nr",
-  ],
-  "blastx": [
-    "env_nr",
-    "landmark"
-    "nr",
-    "pat",
-    "pdb",
-    "refseq_protein",
-    "swissprot",
-    "tsa_nr",
-  ],
-  "tblastn": [
-    "alu_repeats",
-    "Bacteria and Archaea",
-    "chromosome",
-    "dbsts",
-    "est",
-    "gss",
-    "HTGS",
-    "nr/nt",
-    "pat",
-    "pdb",
-    "refseq_gene",
-    "refseq_genomic",
-    "refseq_representative_genomes",
-    "refseq_rna",
-    "SRA",
-    "TSA",
-    "wgs"
-  ],
-  "tblastx": [
-    "alu_repeats",
-    "Bacteria and Archaea",
-    "chromosome",
-    "dbsts",
-    "est",
-    "gss",
-    "HTGS",
-    "nr/nt",
-    "pat",
-    "pdb",
-    "refseq_gene",
-    "refseq_genomic",
-    "refseq_representative_genomes",
-    "refseq_rna",
-    "SRA",
-    "TSA",
-    "wgs"
-  ]
+  "blast_info": {
+    "blastn": [
+      "alu_repeats",
+      "Bacteria and Archaea",
+      "chromosome",
+      "dbsts",
+      "est",
+      "gss",
+      "HTGS",
+      "nt",
+      "pat",
+      "pdb",
+      "refseq_gene",
+      "refseq_genomic",
+      "refseq_representative_genomes",
+      "refseq_rna",
+      "SRA",
+      "TSA",
+      "wgs"
+    ],
+    "blastp": [
+      "env_nr",
+      "landmark",
+      "nr",
+      "pat",
+      "pdb",
+      "refseq_protein",
+      "swissprot",
+      "tsa_nr"
+    ],
+    "blastx": [
+      "env_nr",
+      "landmark",
+      "nr",
+      "pat",
+      "pdb",
+      "refseq_protein",
+      "swissprot",
+      "tsa_nr"
+    ],
+    "tblastn": [
+      "alu_repeats",
+      "Bacteria and Archaea",
+      "chromosome",
+      "dbsts",
+      "est",
+      "gss",
+      "HTGS",
+      "nt",
+      "pat",
+      "pdb",
+      "refseq_gene",
+      "refseq_genomic",
+      "refseq_representative_genomes",
+      "refseq_rna",
+      "SRA",
+      "TSA",
+      "wgs"
+    ],
+    "tblastx": [
+      "alu_repeats",
+      "Bacteria and Archaea",
+      "chromosome",
+      "dbsts",
+      "est",
+      "gss",
+      "HTGS",
+      "nt",
+      "pat",
+      "pdb",
+      "refseq_gene",
+      "refseq_genomic",
+      "refseq_representative_genomes",
+      "refseq_rna",
+      "SRA",
+      "TSA",
+      "wgs"
+    ]
+  }
 }
diff --git a/package-metadata.json b/package-metadata.json
@@ -7,6 +7,6 @@
     ],
     "description": "BioPython Utilities for Sublime Text 3",
     "url": "https://github.com/bosborne/BioPythonUtils",
-    "version": "2017-01-19_12-21"
+    "version": "2017-02-18_12-21"
   }
 }
diff --git a/test/test.fa b/test/test.fa
@@ -129,3 +129,23 @@ IDGWYGFRHQNAEGTGTAADLKSTQAAIDQINGKLNRLIEKTNEKYHQIEKEFEQVEGRI
 QDLEKYVEDTKIDLWSYNAELLVALENQHTIDVTDSEMNKLFERVRRQLRENAEDKGNGC
 FEIFHQCDNNCIESIRNGTYDHDIYRDEAINNRFQIQGVKLTQGYKDIILWISFSISCFL
 LVALLLAFILWACQNGNIRCQICI
+>S000320704 uncultured eubacterium TRA2-10; AF047642
+GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGgtttataagggc
+ttgcccttatagatAGTGGCGAACGGGTGCGTAACACGTGAGCAACCTGCCCCAAAGTTTGGAATAACACCGGGAAACCG
+ATGCTAATACCAAATATGcTCACACTATCACAAGATAGAGTGAgGAAAGTtttTCGCTTTGGGAGGGGCTCGCGGCCTAT
+CAGCTTGTTGGTGAGGTAACGGCTCACCAAGGCATCGACGGGTAGCTGGTCTGAGAGGACGATCAGCCACACTGGGACTG
+AGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCAATGGGCGAAAGCCTGACGCAGCAACGCCGCG
+TGGAGGATGAAGGCCTTAGGGTCGTAAACTCCTTTCAGCAGGAACGAaaaTGACGGTACCTGCAGAAGAAGCTCCGGCCA
+ACTACGTGCCAGCAGCCGCGGTAATACGTAGGGAGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGAGCTCGTAGGCGGC
+TTGGCAAGTCGGATGTGAAACCCCCAGGCTTAACCTGGGGCCGCCATTCGATACTGCTAtGGCTTGAGTTCGGTAGGGGA
+TTGTGGAATTCCCGGTGTAGCGATGAAATGCGCAGATATCGGGAGGAACACCAATGGCGAAGGCAGCAATCTGGGCCGAC
+ACTGACGCTGAGGAGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGTTGGGCACTA
+GGTGTGGGACctacttcgacggGTTCCGTGCCGTAGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGGCCGCAAGGCT
+AAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGCTTAATTCGATGCAACGCGAAGAACCTCACC
+TGGGCTTGACATGTTGGGaAAAGCCGTAGAGATACGGTGtccattagggCCCTT-CACAGGTGGTGCATGGCTGTCGTCA
+GCTCGTGTCGTGAGATGTTGAGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTTATGTTACCAGCGagtaatgtCGGGGA
+CTCATGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTGC
+ACACATGCTACAATGGCCGGTACAGAGGGTCGCAATCCCGCGAGGGGGAGCTAATCCCACAAAGCCGGTCTCAGTTCGGA
+TCGCAGTCTGCAACTCGACTGCGTGAAGCCGGAGTCGCTAGTAATCCCGAATCAGCaTTGTCGGGGTGAATACGTTCCCG
+GGCCTTGTACACACCGCCCGTCACACCACGAAAGTCGGCAACACCCGAAGCCGGTggcccaaccagtaatggagggaGCC
+