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