From 958d9b8aea04c566a3c15ec8af53e806077b67bb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 14 Aug 2019 13:09:59 -0500
Subject: Genome browser now takes chromosome list and lengths as input so it
 will work correctly with non-mouse species or centimorgan positions

---
 wqflask/wqflask/marker_regression/run_mapping.py   | 29 +++++++++++++++++++++-
 .../static/new/javascript/init_genome_browser.js   | 23 +----------------
 2 files changed, 29 insertions(+), 23 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 20c5c5bd..1c08d653 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -365,6 +365,8 @@ class RunMapping(object):
               with Bench("Trimming Markers for Table"):
                   self.trimmed_markers = trim_markers_for_table(results)
 
+              chr_lengths = get_chr_lengths(self.mapping_scale, self.dataset, self.qtl_results_for_browser)
+
               if self.mapping_method != "gemma":
                   if self.score_type == "LRS":
                       significant_for_browser = self.significant / 4.16
@@ -380,6 +382,7 @@ class RunMapping(object):
                       #mapping_scale = self.mapping_scale,
                       #chromosomes = chromosome_mb_lengths,
                       #qtl_results = self.qtl_results,
+                      chr_lengths = chr_lengths,
                       num_perm = self.num_perm,
                       perm_results = self.perm_output,
                       browser_files = browser_files,
@@ -387,6 +390,7 @@ class RunMapping(object):
                   )
               else:
                 self.js_data = dict(
+                    chr_lengths = chr_lengths,
                     browser_files = browser_files
                 )
 
@@ -535,4 +539,27 @@ def geno_db_exists(this_dataset):
         geno_db = data_set.create_dataset(dataset_name=geno_db_name, get_samplelist=False)
         return "True"
     except:
-        return "False"
\ No newline at end of file
+        return "False"
+
+def get_chr_lengths(mapping_scale, dataset, qtl_results):
+    chr_lengths = []
+    if mapping_scale == "physic":
+        for i, the_chr in enumerate(dataset.species.chromosomes.chromosomes):
+            this_chr = {
+                "chr": dataset.species.chromosomes.chromosomes[the_chr].name,
+                "size": str(dataset.species.chromosomes.chromosomes[the_chr].length)
+            }
+            chr_lengths.append(this_chr)
+    else:
+        this_chr = 1
+        highest_pos = 0
+        for i, result in enumerate(qtl_results):
+            if int(result['chr']) > this_chr or i == (len(qtl_results) - 1):
+                chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)})
+                this_chr = int(result['chr'])
+                highest_pos = 0
+            else:
+                if float(result['ps']) > highest_pos:
+                    highest_pos = float(result['ps'])
+
+    return chr_lengths
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
index 7dfd6712..a544f3cb 100644
--- a/wqflask/wqflask/static/new/javascript/init_genome_browser.js
+++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
@@ -9,28 +9,7 @@ localUrls =
   annotations: annot_filename
 };
 
-var coordinateSystem =
-          [
-              { chr: "1", size: "195471971" },
-              { chr: "2", size: "182113224" },
-              { chr: "3", size: "160039680" },
-              { chr: "4", size: "156508116" },
-              { chr: "5", size: "151834684" },
-              { chr: "6", size: "149736546" },
-              { chr: "7", size: "145441459" },
-              { chr: "8", size: "129401213" },
-              { chr: "9", size: "124595110" },
-              { chr: "10", size: "130694993" },
-              { chr: "11", size: "122082543" },
-              { chr: "12", size: "120129022" },
-              { chr: "13", size: "120421639" },
-              { chr: "14", size: "124902244" },
-              { chr: "15", size: "104043685" },
-              { chr: "16", size: "98207768" },
-              { chr: "17", size: "94987271" },
-              { chr: "18", size: "90702639" },
-              { chr: "19", size: "61431566" },
-          ];
+var coordinateSystem = js_data.chr_lengths
 
 var vscaleWidth = 90.0;
 var legendWidth = 140.0;
-- 
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