git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@87 60f365c0-8329-0410-b2a4-ec073aeeaa1d

tools/ecoSort.py

@@ -5,11 +5,16 @@ import sys
 import os
 import gzip
 import re
+import string
 
 from reportlab.graphics.shapes import *
 from reportlab.graphics.charts.barcharts import VerticalBarChart
 from reportlab.graphics.charts.piecharts import Pie
-from reportlab.graphics import renderPDF
+from reportlab.lib.styles import getSampleStyleSheet
+from reportlab.lib.units import cm
+from reportlab.lib import colors
+from reportlab.platypus import *
+
 
 #####
 #
@@ -337,7 +342,7 @@ class ColumnFile(object):
 ###########
 
 
-class Table(list):
+class ecoTable(list):
     """
         Data object inheriting from list
     """
@@ -364,59 +369,113 @@ class Table(list):
 ###########
 
 
-def _makeHistogram(data,label,title,path):
-    
-    drawing = Drawing(350, 450)
-    
-    drawing.add(String(35,430,title,fontSize=10))
-    
-    bc = VerticalBarChart()
-    bc.x = 40
-    bc.y = 100
-    bc.height = 300
-    bc.width = 300
-    bc.bars.strokeWidth = 1
-    bc.barSpacing = 2
-    bc.barLabelFormat = '%d'
-    bc.barLabels.dy = -5
-    bc.barLabels.fontSize = 9 - (len(data[0])/8)
-    bc.data = data
-       
-    bc.valueAxis.valueMin = min(data[0])*0.7
-    bc.valueAxis.valueMax = max(data[0])
-    bc.valueAxis.valueStep = (max(data[0]) - min(data[0])) / 10
-    bc.valueAxis.strokeWidth = 1
-    
-    bc.categoryAxis.labels.boxAnchor = 'e'
-    bc.categoryAxis.labels.dx = -40
-    bc.categoryAxis.labels.dy = -50
-    bc.categoryAxis.labels.angle = 45
-    bc.categoryAxis.labels.width = 10
-    bc.categoryAxis.labels.height = 4
-    bc.categoryAxis.categoryNames = label
-    bc.categoryAxis.strokeWidth = 1
-    bc.categoryAxis.labels.fontSize = 9
 
 
-    drawing.add(bc)
+def drawGraphs(data,path='graph.pdf'):
+    """
+      Generate a pdf file with graph illustrating the data given as
+      arguments. Takes two arguments :
+      1- an array of array. Each element contains :
+          * Table object
+          * number of columns 1 and 2 to be ploted
+          * a Title
+          * Number of element to be ploted (10 by default)
+          * type of graph (1 for histogram or 2 for pie)   
+      2- path of file-to-be (graph.pdf by default)
+    """
+    
+    def box(flt, center=True):
+        box_style = [('BOX', (0, 0), (-1, -1), 0.5, colors.lightgrey)]
+        if center:
+            box_style += [('ALIGN', (0, 0), (-1, -1), 'CENTER')]
+        return Table([[flt]], style=box_style)
+     
+    def makeHistogram(data,label):    
+        
+        c = VerticalBarChart() 
+        c.x = 10 
+        c.y = 70 
+        c.height = 150 
+        c.width = 300
+        c.bars.strokeWidth = 1
+        c.barSpacing = 1
+        c.barLabels.dy = 5
+        c.barLabelFormat = '%d'
+        c.barLabels.fontSize = 9 - (len(data[0])/10)
+        c.data = data
+        
+        c.categoryAxis.labels.boxAnchor = 'e'
+        c.categoryAxis.labels.textAnchor = 'start'        
+        c.categoryAxis.labels.dx = -40
+        c.categoryAxis.labels.dy = -50
+        c.categoryAxis.labels.angle = 45
+        c.categoryAxis.labels.width = 10
+        c.categoryAxis.labels.height = 4
+        c.categoryAxis.categoryNames = label
+        c.categoryAxis.strokeWidth = 1
+        c.categoryAxis.labels.fontSize = 8
+        
+        
+        c.valueAxis.valueMin = min(data[0])*0.7 
+        c.valueAxis.valueMax = max(data[0])
+        step = (max(data[0]) - min(data[0])) / 10
+        c.valueAxis.valueStep = step > 1 and step or 1
+        
+        
+        return c
+
+
+    def makePie(data, label):
+       
+        c = Pie()
+        c.x = 100
+        c.y = 100
+        c.data = data
+        c.labels = label   
+        return c
+   
+    styles = getSampleStyleSheet()
+    doc = SimpleDocTemplate(path)
+    
+    elements = []
+    elements.append(box(Paragraph("EcoPCR report", styles['Title'])))
+    elements.append(Spacer(0, 0.5 * cm))
+
+    for e in data:
+        count, label = [], []
+        table = e[0]
+        col1, col2  = e[1]-1, e[2]-1
+        title = e[3]
+        try:   
+            treshold = e[4]
+        except:
+            treshold = 10
+        try:
+            graphType= e[5]
+        except:
+            graphType= 1
+        
+        for i in range(treshold):
+            count.append(table[i][col2])
+            label.append(table[i][col1])
+      
+        elements.append(box(Paragraph(title, styles['Normal'])))
+        if graphType == 2:
+            chart = makePie(count,label)
+        else:
+            chart = makeHistogram([tuple(count)],label)
+        drawing = Drawing(300, 250)
+        drawing.add(chart)
+        elements.append(box(drawing))
+        elements.append(Spacer(0, 2 * cm))
+
+    doc.build(elements)
 
-    renderPDF.drawToFile(drawing, path )
 
-def _makePie(data, label, title, path):
 
-    drawing = Drawing(400,400)
-    drawing.add(String(50,50,title,fontSize=10))
 
-    pc = Pie()
-    pc.x = 100
-    pc.y = 100
-    pc.data = data
-    pc.labels = label
-    pc.labels.angle = 45
     
-    drawing.add(pc)
 
-    renderPDF.drawToFile(drawing,path)
     
     
 ###########
@@ -499,7 +558,7 @@ def customSort(table,x,y):
     y = y-1
     h = (table.headers[x],table.headers[y])
     t = (table.types[x],table.types[y])
-    cTable = Table(h,t)
+    cTable = ecoTable(h,t)
     
     tmp = {}
     
@@ -538,7 +597,7 @@ def countColumnOccurrence(table,x):
 def buildSpecificityTable(table):
     header =  ("mismatch","taxon","count")
     type = (int,str,int)
-    speTable = Table(header,type)
+    speTable = ecoTable(header,type)
     
     tmp = {}
     for l in table:
@@ -580,7 +639,7 @@ def buildOligoTable(table, file, filter, oligoRef, strand='direct'):
         table[i]=[oligo,count,lctTaxid,scName,rank,mismatch]
         i = i + 1
         
-    table.sort(sortTable)
+    table.sort(_sortTable)
 
  
 def buildTaxonomicTable(table):
@@ -589,7 +648,7 @@ def buildTaxonomicTable(table):
     """
     taxHeaders = ("scName","numOfOligo","numOfAmpl","taxid")
     taxTypes = (str, int, int, int)
-    taxTable = Table(taxHeaders, taxTypes)
+    taxTable = ecoTable(taxHeaders, taxTypes)
     
     tax = _parseTaxonomyResult(table) 
   
@@ -600,7 +659,7 @@ def buildTaxonomicTable(table):
         taxTable[i]=[scName,numOfOligo,numOfAmpl,taxid]
         i = i + 1 
 
-    taxTable.sort(sortTable)
+    taxTable.sort(_sortTable)
 
     return taxTable
 
@@ -721,13 +780,13 @@ def grepTable(table,col,pattern):
     """
     col = col -1
     p = re.compile(pattern, re.IGNORECASE)
-    out = Table(table.headers,table.types)
+    out = ecoTable(table.headers,table.types)
     for l in table:
         if p.search(l[col]):
             out.append(l)
     return out
 
-def drawGraph(table,x,y,path='graph.pdf',title='',treshold=10,graphType=1):
+def drawGraph(data,path='graph.pdf'):
     """
         Creates an histogram as pdf file
         Takes 5 arguments :
@@ -739,18 +798,31 @@ def drawGraph(table,x,y,path='graph.pdf',title='',treshold=10,graphType=1):
         6- the x first highest results (10 by default)
         7- the graph type : 1 for histogram, 2 for pie
     """
+    drawing = Drawing(350, 450)
+    
+   
+    
+    for e in data:
         count, label = [], []
-    x = x-1
+        table = e[0]
-    y = y-1
+        col1 = e[1]-1
+        col2 = e[2]-1
+        title = e[3]
+        treshold = e[4]
+        graphType= e[5]
+        
         for l in table:
             count.append(l[y])
             label.append(str(l[x]))
         if graphType == 1:
-        _makeHistogram([tuple(count[:treshold])], label[:treshold], title, path)
+            graph = _makeHistogram([tuple(count[:treshold])], label[:treshold], title, path)
         elif graphType == 2:
             _makePie(count[:treshold], label[:treshold], title, path)
 
+        drawing.add(String(35,430,title,fontSize=10))
+        drawing.add(graph)
     
+    renderPDF.drawToFile(drawing, path )
 
 ###################### 
 
@@ -761,28 +833,24 @@ def init():
      
     filter = Filter("/ecoPCRDB/gbmam")
     
-#    headers = ("oligo", "Num", "LCT Taxid", "Sc Name", "Rank", "distance")
+    headers = ("oligo", "Num", "LCT Taxid", "Sc Name", "Rank", "distance")
-#    types = (str, int, int, str, str, int)
+    types = (str, int, int, str, str, int)
-#    
+    
-#    o1Table = Table(headers, types)
+    o1Table = ecoTable(headers, types)
-#    o2Table = Table(headers, types)
+    o2Table = ecoTable(headers, types)
-#    
+    
-#    buildOligoTable(o1Table, file, filter, oligo['o1'], 'direct')
+    buildOligoTable(o1Table, file, filter, oligo['o1'], 'direct')
-#    buildOligoTable(o2Table, file, filter, oligo['o2'], 'reverse')
+    buildOligoTable(o2Table, file, filter, oligo['o2'], 'reverse')
-#
+
-# 
+ 
-#    taxTable = buildTaxonomicTable(o1Table)
+    taxTable = buildTaxonomicTable(o1Table)
-#    speTable = buildSpecificityTable(o1Table)
+    speTable = buildSpecificityTable(o1Table)
+   
 #   
+#    seqHeaders = ("sequence","taxid")
+#    seqTypes = (str,list) 
+#    seqTable = Table(seqHeaders,seqTypes)
     
-    seqHeaders = ("sequence","taxid")
+    return o1Table, o2Table, taxTable
-    seqTypes = (str,list) 
-    seqTable = Table(seqHeaders,seqTypes)
-    
-    return buildSequenceTable(seqTable, file, filter)
-    
-    
-
-    return seqTable