backend blast new almost ready

voseq/blast_new/utils.py

@@ -4,6 +4,7 @@
 from Bio import SeqIO
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
+from django.db.models import Q
 
 from blast_local.utils import BLAST
 from public_interface.models import Sequences
@@ -47,3 +48,48 @@ def __init__(self, blast_type, name, sequence, gene_codes, mask=None):
                                         'db',
                                         'output_' + uuid.uuid4().hex + '.xml',
                                         )
+
+    def save_seqs_to_file(self):
+        """
+        Query sequences for each gene from our database and save them to local
+        disk.
+
+        Sets attribute `self.seq_file` containing necessary sequences from our
+        database.
+        """
+        if self.blast_type == 'new':
+            self.seq_file = os.path.join(self.cwd,
+                                         'db',
+                                         '_'.join(self.gene_codes) + "_seqs.fas",
+                                         )
+            if self.gene_codes != '':
+                # Taken from http://stackoverflow.com/a/1239602
+                Qr = None
+                for gene_code in self.gene_codes:
+                    q = Q(gene_code=gene_code)
+                    if Qr:
+                        Qr = Qr | q
+                    else:
+                        Qr = q
+                queryset = Sequences.objects.filter(Qr)
+            else:
+                queryset = Sequences.objects.all()
+
+            my_records = []
+            for i in queryset:
+                id = i.code_id + '|' + i.gene_code
+                seq = self.strip_question_marks(i.sequences)
+                if seq != '':
+                    seq_record = SeqRecord(Seq(seq),
+                                           id=id)
+                    my_records.append(seq_record)
+            SeqIO.write(my_records, self.seq_file, "fasta")
+
+    def save_query_to_file(self):
+        this_id = self.name
+        seq = self.strip_question_marks(self.sequence)
+
+        if seq != '':
+            seq_record = SeqRecord(Seq(seq),
+                                   id=this_id)
+            SeqIO.write(seq_record, self.query_file, "fasta")

voseq/blast_new/views.py

@@ -2,6 +2,7 @@
 from django.conf import settings
 from django.http import HttpResponseRedirect
 
+from .utils import BLASTNew
 from stats.models import Stats
 from .forms import BLASTNewForm
 
@@ -24,11 +25,37 @@ def index(request):
 
 
 def results(request):
+    VERSION = settings.VERSION
+    try:
+        STATS = Stats.objects.get(pk=1)
+    except Stats.DoesNotExist:
+        STATS = ''
+
     if request.method == 'POST':
         form = BLASTNewForm(request.POST)
+
         if form.is_valid():
-            print(request.POST)
-            return render(request,
-                          'blast_new/results.html')
+            cleaned_data = form.cleaned_data
+
+            # tmp, remove after fixing form
+            cleaned_data['gene_codes'] = ''
+            blast = BLASTNew('new', cleaned_data['name'], cleaned_data['sequence'],
+                             cleaned_data['gene_codes'])
+            blast.save_seqs_to_file()
+
+            if blast.is_blast_db_up_to_date() is False:
+                blast.create_blast_db()
+
+            blast.save_query_to_file()
+            blast.do_blast()
+            result = blast.parse_blast_output()
+            blast.delete_query_output_files()
+            return render(request, 'blast_new/results.html',
+                          {
+                              'result': result,
+                              'version': VERSION,
+                              'stats': STATS,
+                          },
+                          )
 
     return HttpResponseRedirect('/blast_new/')