#78 dice_self_contigs for large chromosomes, inserting fake entries. …

…Mouse retreival changed to work with streaming.

DDV/TileLayout.py

@@ -247,12 +247,14 @@ def draw_nucleotides(self, verbose=True):
 
 
     def output_fasta(self, output_folder, fasta, no_webpage, extract_contigs, sort_contigs, append_fasta_sources=True):
+        """This method is destructive.  It does not preserve the original self.contigs"""
         bare_file = os.path.basename(fasta)
         if append_fasta_sources:
             self.fasta_sources.append(bare_file)
 
         #also make single file
         if not no_webpage:
+            self.dice_self_contigs(1000000)
             write_contigs_to_chunks_dir(output_folder, bare_file, self.contigs)
             self.remember_contig_spacing()
             fasta_destination = os.path.join(output_folder, 'sources', bare_file)
@@ -541,10 +543,13 @@ def contig_struct(self):
                 break  # I don't want to use a slice operator on the for loop because that will copy it
             xy_seq_start += contig.reset_padding + contig.title_padding
             xy_seq_end = xy_seq_start + len(contig.seq)
-            json.append({"name": contig.name.replace("'", ""), "xy_seq_start": xy_seq_start, "xy_seq_end": xy_seq_end,
-                         "title_padding": contig.title_padding, "tail_padding": contig.tail_padding,
-                         "xy_title_start": xy_seq_start - contig.title_padding,
-                         "nuc_title_start": contig.nuc_title_start, "nuc_seq_start": contig.nuc_seq_start})
+            fake_start = 0 if not hasattr(contig, 'fake_start') else contig.fake_start
+            json.append(
+                {"name": contig.name.replace("'", ""), "xy_seq_start": xy_seq_start, "xy_seq_end": xy_seq_end,
+                 "title_padding": contig.title_padding, "tail_padding": contig.tail_padding,
+                 "xy_title_start": xy_seq_start - contig.title_padding,
+                 "nuc_title_start": contig.nuc_title_start, "nuc_seq_start": contig.nuc_seq_start,
+                 "fake_start": fake_start})
             xy_seq_start += len(contig.seq) + contig.tail_padding
         return json
 
@@ -600,6 +605,27 @@ def all_layouts_json(self):
     def remember_contig_spacing(self):
         self.contig_memory.append(self.contig_struct())
 
+    def dice_self_contigs(self, chunk_size):
+        for i in reversed(range(len(self.contigs))):
+            print(i, end='')
+            if len(self.contigs[i].seq) > chunk_size:
+                temp = self.contigs[i]
+                positions= range(0, len(temp.seq), chunk_size)
+                self.contigs[i:i+1] = [ContigChunk(temp, start, chunk_size) for start in positions]
+
+
+class ContigChunk(Contig):
+    def __init__(self, original, fake_start, size):
+        super(ContigChunk, self).__init__(original.name, original.seq[fake_start: fake_start+size])
+        self.fake_start=fake_start
+        at_the_end = len(self.seq) != size
+        first_chunk = not fake_start
+        self.title_padding = original.title_padding if first_chunk else 0
+        self.nuc_title_start = original.nuc_title_start if first_chunk else fake_start
+        self.nuc_seq_start = original.nuc_seq_start + fake_start
+        self.tail_padding = original.tail_padding if at_the_end else 0
+        self.reset_padding = original.reset_padding if at_the_end else 0
+
 
 def write_contigs_to_chunks_dir(project_dir, fasta_name, contigs):
     chunks_dir = os.path.join(project_dir, 'chunks', fasta_name)

DDV/fluentdna.py

@@ -121,7 +121,7 @@ def done(args, output_dir):
     Otherwise system exit."""
     if args.run_server:
         run_server(output_dir)
-    # beep()
+    beep()
     hold_console_for_windows()
     if __name__ == "__main__":
         sys.exit(0)

DDV/html_template/nucleotideNumber.js

@@ -251,8 +251,8 @@ function showNucleotideNumber(event, viewer) {
                 start = Nucleotide - 1;
                 stop = Nucleotide;
             }
-            if(contigs[position_info.fasta_index].hasOwnProperty(position_info.contig_name)){
-                theSequence = contigs[position_info.fasta_index][position_info.contig_name].substring(start, stop);
+            if(contigs[position_info.fasta_index].hasOwnProperty(position_info.contig_index)){
+                theSequence = contigs[position_info.fasta_index][position_info.contig_index].substring(start, stop);
                 //theSequence = theSequence.replace(/\s+/g, '')
                 fragmentid = position_info.contig_name + ": (" +
                   numberWithCommas(start + 1) + " - " + numberWithCommas(stop) + ")";
@@ -334,21 +334,22 @@ function getSequence(fasta_index, contig_index) {
             contentType: "text/html",
             success: function (sequence_received) {
                 file_transfer_in_progress = false;
-                read_contigs(sequence_received, fasta_index);
+                read_contigs(sequence_received, fasta_index, contig_index);
             },
             error: processInitSequenceError
         });
     }
 }
 
-function read_contigs(sequence_received, fasta_index) {
+function read_contigs(sequence_received, fasta_index, contig_index) {
     //read_contigs equiv in javascript
     theSequenceSplit = sequence_received.split(/\r?\n(?=>)/);// begin line, caret  ">");
-    for (let contig_s of theSequenceSplit) {
-        var lines = contig_s.split(/\r?\n/);
-        var title = lines[0].slice(1)
+    //for (var contig_index =0; contig_index < theSequenceSplit.length; contig_index++)
+    {//Each chunk file is only one contig, no need to loop
+        var lines = theSequenceSplit[0].split(/\r?\n/);
+        //var title = lines[0].slice(1)
         var seq = lines.slice(1).join('');
-        contigs[fasta_index][title] = seq;
+        contigs[fasta_index][contig_index] = seq;
     }
     return contigs
 }