From: Rami Rauch <rrauch@stanford.edu>
Date: Tue, 7 Oct 2008 21:56:06 +0000 (+0000)
Subject: Added a display column (not DB) to show the total count of alligned reads for each... 
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=7e2817f11e42fdc5aa33cf310bc50e6346bed3ca

Added a display column (not DB) to show the total count of alligned reads for each library record
---

diff --git a/htswfrontend/htswfrontend/fctracker/models.py b/htswfrontend/htswfrontend/fctracker/models.py
index 3dfd513..b7d3abd 100644
--- a/htswfrontend/htswfrontend/fctracker/models.py
+++ b/htswfrontend/htswfrontend/fctracker/models.py
@@ -1,5 +1,6 @@
 from django.db import models
 from htswfrontend import settings
+from htswfrontend.htsw_reports.libinfopar import *
 
 class Primer(models.Model):
   primer_name = models.CharField(max_length=100, db_index=True)
@@ -170,11 +171,14 @@ class Library(models.Model):
   
   class Meta:
     verbose_name_plural = "libraries"
-    ordering = ["-library_id"]
+    ordering = ["-creation_date"] #["-library_id"]
   
   def antibody_name(self):
     return self.antibody.nickname
 
+  def org(self):
+    return self.library_species.common_name
+
   def affiliation(self):
     affs = self.affiliations.all().order_by('name')
     tstr = ''
@@ -183,13 +187,39 @@ class Library(models.Model):
         ar.append(t.__str__())
     return '%s' % (", ".join(ar))
 
+
+  def aligned_reads(self):
+    res = getLibReads(self.library_id)
+    rc = "%1.2f" % (res[1]/1000000.0)
+    # Color Scheme: green is more than 10M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds should be doubled
+    if res[0] > 0:
+      bgcolor = '#ff3300'  # Red
+      rc_thr = [10000000,5000000,3000000]
+      if self.experiment_type == 'RNA-seq':
+        rc_thr = [20000000,10000000,6000000]
+
+      if res[1] > rc_thr[0]:
+        bgcolor = '#66ff66'  # Green
+      else:
+        if res[1] > rc_thr[1]:
+          bgcolor ='#00ccff'  # Blue
+        else:
+           if res[1] > rc_thr[2]: 
+             bgcolor ='#ffcc33'  # Orange
+      tstr = '<div style="background-color:'+bgcolor+';color:black">'
+      tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
+      tstr += '</div>'
+    else: tstr = 'not processed yet' 
+    return tstr
+  aligned_reads.allow_tags = True
+
   class Admin:
     date_hierarchy = "creation_date"
     save_as = True
     save_on_top = True
     ##search_fields = ['library_id','library_name','affiliations__name','affiliations__contact','made_by','made_for','antibody__antigene','antibody__catalog','antibody__antibodies','antibody__source','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
     search_fields = ['library_id','library_name','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
-    list_display = ('affiliation','library_id', 'library_name','experiment_type','replicate','antibody_name','cell_line','made_by','creation_date')
+    list_display = ('affiliation','library_id','aligned_reads','library_name','experiment_type','org','replicate','antibody_name','cell_line','made_by','creation_date')
     list_display_links = ('library_id', 'library_name')
     list_filter = ('experiment_type','affiliations','library_species','made_for', 'made_by','replicate')
     fields = (