git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@88 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
315
tools/ecoSort.py
315
tools/ecoSort.py
@ -359,125 +359,26 @@ class ecoTable(list):
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for e in range(len(value)):
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for e in range(len(value)):
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value[e] = self.types[e](value[e])
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value[e] = self.types[e](value[e])
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list.__setitem__(self,key,value)
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list.__setitem__(self,key,value)
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###########
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#
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# GRAPH FUNCTIONS
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#
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###########
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def drawGraphs(data,path='graph.pdf'):
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"""
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Generate a pdf file with graph illustrating the data given as
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arguments. Takes two arguments :
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1- an array of array. Each element contains :
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* Table object
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* number of columns 1 and 2 to be ploted
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* a Title
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* Number of element to be ploted (10 by default)
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* type of graph (1 for histogram or 2 for pie)
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2- path of file-to-be (graph.pdf by default)
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"""
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def box(flt, center=True):
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box_style = [('BOX', (0, 0), (-1, -1), 0.5, colors.lightgrey)]
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if center:
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box_style += [('ALIGN', (0, 0), (-1, -1), 'CENTER')]
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return Table([[flt]], style=box_style)
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def makeHistogram(data,label):
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c = VerticalBarChart()
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def __getitem__(self,index):
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c.x = 10
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newtable = ecoTable(self.headers,self.types)
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c.y = 70
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if isinstance(index,slice):
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c.height = 150
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newtable.extend(list.__getitem__(self,index))
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c.width = 300
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c.bars.strokeWidth = 1
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c.barSpacing = 1
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c.barLabels.dy = 5
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c.barLabelFormat = '%d'
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c.barLabels.fontSize = 9 - (len(data[0])/10)
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c.data = data
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c.categoryAxis.labels.boxAnchor = 'e'
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c.categoryAxis.labels.textAnchor = 'start'
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c.categoryAxis.labels.dx = -40
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c.categoryAxis.labels.dy = -50
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c.categoryAxis.labels.angle = 45
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c.categoryAxis.labels.width = 10
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c.categoryAxis.labels.height = 4
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c.categoryAxis.categoryNames = label
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c.categoryAxis.strokeWidth = 1
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c.categoryAxis.labels.fontSize = 8
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c.valueAxis.valueMin = min(data[0])*0.7
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c.valueAxis.valueMax = max(data[0])
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step = (max(data[0]) - min(data[0])) / 10
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c.valueAxis.valueStep = step > 1 and step or 1
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return c
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def makePie(data, label):
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c = Pie()
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c.x = 100
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c.y = 100
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c.data = data
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c.labels = label
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return c
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styles = getSampleStyleSheet()
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doc = SimpleDocTemplate(path)
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elements = []
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elements.append(box(Paragraph("EcoPCR report", styles['Title'])))
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elements.append(Spacer(0, 0.5 * cm))
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for e in data:
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count, label = [], []
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table = e[0]
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col1, col2 = e[1]-1, e[2]-1
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title = e[3]
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try:
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treshold = e[4]
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except:
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treshold = 10
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try:
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graphType= e[5]
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except:
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graphType= 1
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for i in range(treshold):
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count.append(table[i][col2])
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label.append(table[i][col1])
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elements.append(box(Paragraph(title, styles['Normal'])))
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if graphType == 2:
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chart = makePie(count,label)
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else:
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else:
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chart = makeHistogram([tuple(count)],label)
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newtable.append(list.__getitem__(self,index))
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drawing = Drawing(300, 250)
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drawing.add(chart)
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return newtable
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elements.append(box(drawing))
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elements.append(Spacer(0, 2 * cm))
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doc.build(elements)
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def getColumns(self,columnList):
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newhead = [self.headers[x] for x in columnList]
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newtype = [self.types[x] for x in columnList]
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newtable = ecoTable(newhead,newtype)
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for line in self:
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newtable.append([line[x] for x in columnList])
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return newtable
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###########
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###########
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#
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#
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# PARSE FUNCTIONS
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# PARSE FUNCTIONS
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@ -693,7 +594,7 @@ def _sameValuesInList(array):
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return True
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return True
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def buildSequenceTable(table,file,filter):
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def _sortSequences(file,filter):
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sequences, idIndex = _parseSequenceResult(filter,file,'species')
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sequences, idIndex = _parseSequenceResult(filter,file,'species')
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@ -701,24 +602,37 @@ def buildSequenceTable(table,file,filter):
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if len(id) == 1 or _sameValuesInList(id):
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if len(id) == 1 or _sameValuesInList(id):
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idIndex[id[0]].append(1)
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idIndex[id[0]].append(1)
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else:
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else:
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idIndex[id[0]].append(0)
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for e in id:
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idIndex[e].append(0)
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for id,values in idIndex.items():
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for id,values in idIndex.items():
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c = values.count(1)
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idIndex[id] = float(values.count(1)) / float(len(values)) * 100
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if c == 0:
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idIndex[id] = -1
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else:
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idIndex[id] = len(values) == c and 1 or 0
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identified = {}
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identified = {}
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non_identified = {}
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non_identified = {}
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ambiguous = {}
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ambiguous = {}
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return sequences, idIndex
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def getIntraSpeciesDiversity(table,file,filter):
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for sequence in sequences:
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intraDiv = {}
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pass
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seq, idIndex = _sortSequences(file,filter)
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for id,percent in idIndex.items():
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if percent == 100:
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intraDiv[id] = [0,[]]
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for seq,idList in sequences.items():
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if id in idList:
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intraDiv[id][0] = intraDiv[id][0] + 1
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intraDiv[id][1].append(seq)
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for id, values in intraDiv.items():
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table.append(id,values[0],values[1])
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###########
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###########
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@ -739,20 +653,7 @@ def printTable(table):
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for l in table:
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for l in table:
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print format % tuple([str(e) for e in l ])
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print format % tuple([str(e) for e in l ])
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print "# %d results" % len(table)
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print "# %d results" % len(table)
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def printColumn(table,n):
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"""
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Displays a column of a Table object
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Takes 2 arguments
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1- Table object
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2- Number of the Column to display
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"""
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n = n - 1
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print "\t%s\n" % table.headers[n]
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for l in table:
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print "%s" % l[n]
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def saveAsCSV(table,path):
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def saveAsCSV(table,path):
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"""
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"""
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@ -786,44 +687,90 @@ def grepTable(table,col,pattern):
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out.append(l)
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out.append(l)
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return out
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return out
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def drawGraph(data,path='graph.pdf'):
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"""
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###########
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Creates an histogram as pdf file
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#
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Takes 5 arguments :
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# GRAPH FUNCTIONS
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1- a Table object
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#
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2- number of column of Table object for y axis
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###########
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3- number of column of Table object for x axis
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4- path of the pdf-to-be
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class EcoGraph(object):
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5- a title for the graph (optional)
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6- the x first highest results (10 by default)
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7- the graph type : 1 for histogram, 2 for pie
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"""
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drawing = Drawing(350, 450)
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def __init__(self):
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self._styles = getSampleStyleSheet()
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for e in data:
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count, label = [], []
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table = e[0]
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col1 = e[1]-1
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col2 = e[2]-1
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title = e[3]
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treshold = e[4]
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graphType= e[5]
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for l in table:
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self._element = []
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count.append(l[y])
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self._element.append(self._box(Paragraph("EcoPCR report", self._styles['Title'])))
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label.append(str(l[x]))
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self._element.append(Spacer(0, 0.5 * cm))
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if graphType == 1:
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graph = _makeHistogram([tuple(count[:treshold])], label[:treshold], title, path)
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elif graphType == 2:
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_makePie(count[:treshold], label[:treshold], title, path)
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drawing.add(String(35,430,title,fontSize=10))
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drawing.add(graph)
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renderPDF.drawToFile(drawing, path )
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def _box(self,flt, center=True):
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box_style = [('BOX', (0, 0), (-1, -1), 0.5, colors.lightgrey)]
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if center:
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box_style += [('ALIGN', (0, 0), (-1, -1), 'CENTER')]
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return Table([[flt]], style=box_style)
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def _addChart(self,chart,title):
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drawing = Drawing(300, 250)
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drawing.add(chart)
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self._element.append(self._box(Paragraph(title, self._styles['Normal'])))
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self._element.append(self._box(drawing))
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self._element.append(Spacer(0, 0.5 * cm))
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def _formatData(self,table):
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data, label = [],[]
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for i in range(len(table)):
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label.append(table[i][0])
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data.append(table[i][1])
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return data, label
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def makePie(self, table, title):
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data, label = self._formatData(table)
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pie = Pie()
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pie.x = 100
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pie.y = 100
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pie.data = data
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pie.labels = label
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self._addChart(pie, title)
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def makeHistogram(self, table, title):
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data, label = self._formatData(table)
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data = [tuple(data)]
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histo = VerticalBarChart()
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histo.x = 10
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histo.y = 70
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histo.height = 150
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histo.width = 300
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histo.bars.strokeWidth = 1
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histo.barSpacing = 1
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histo.barLabels.dy = 5
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histo.barLabelFormat = '%d'
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histo.barLabels.fontSize = 9 - (len(data[0])/10)
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histo.data = data
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histo.categoryAxis.labels.boxAnchor = 'e'
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histo.categoryAxis.labels.textAnchor = 'start'
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histo.categoryAxis.labels.dx = -40
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histo.categoryAxis.labels.dy = -50
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histo.categoryAxis.labels.angle = 45
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histo.categoryAxis.labels.width = 10
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histo.categoryAxis.labels.height = 4
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histo.categoryAxis.categoryNames = label
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histo.categoryAxis.strokeWidth = 1
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histo.categoryAxis.labels.fontSize = 8
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histo.valueAxis.valueMin = min(data[0])*0.7
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histo.valueAxis.valueMax = max(data[0])
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step = (max(data[0]) - min(data[0])) / 10
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histo.valueAxis.valueStep = step > 1 and step or 1
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self._addChart(histo, title)
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def makeReport(self,path):
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doc = SimpleDocTemplate(path)
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doc.build(self._element)
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######################
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######################
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@ -845,12 +792,20 @@ def init():
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taxTable = buildTaxonomicTable(o1Table)
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taxTable = buildTaxonomicTable(o1Table)
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speTable = buildSpecificityTable(o1Table)
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speTable = buildSpecificityTable(o1Table)
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#
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# seqHeaders = ("sequence","taxid")
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# seqTypes = (str,list)
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# seqTable = Table(seqHeaders,seqTypes)
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return o1Table, o2Table, taxTable
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return o1Table, o2Table, taxTable
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def start():
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file = "/Users/bessiere/Documents/workspace/ecoPCR/src/toto.tmp"
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filter = Filter("/ecoPCRDB/gbmam")
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speHeaders = ("taxid","num of seq","list of seq")
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speTypes = (int,int,list)
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speTable = ecoTable(speHeaders,speTypes)
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getIntraSpeciesDiversity(speTable, file, filter)
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Reference in New Issue
Block a user