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

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Eric Coissac
2007-06-29 12:04:27 +00:00
parent 9fe0c1ce48
commit ddcf0c2fc4
1 changed files with 157 additions and 89 deletions
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246
tools/ecoSort.py
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@ -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):
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)
"""
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
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):
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
c = Pie()
c.x = 100
c.y = 100
c.data = data
c.labels = label
return c
styles = getSampleStyleSheet()
doc = SimpleDocTemplate(path)
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
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)
drawing.add(bc)
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
"""
count, label = [], []
x = x-1
y = y-1
for l in table:
count.append(l[y])
label.append(str(l[x]))
if graphType == 1:
_makeHistogram([tuple(count[:treshold])], label[:treshold], title, path)
elif graphType == 2:
_makePie(count[:treshold], label[:treshold], title, path)
drawing = Drawing(350, 450)
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]
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)
renderPDF.drawToFile(drawing, path )
######################
@ -761,28 +833,24 @@ def init():
filter = Filter("/ecoPCRDB/gbmam")
# headers = ("oligo", "Num", "LCT Taxid", "Sc Name", "Rank", "distance")
# types = (str, int, int, str, str, int)
#
# o1Table = Table(headers, types)
# o2Table = Table(headers, types)
#
# buildOligoTable(o1Table, file, filter, oligo['o1'], 'direct')
# buildOligoTable(o2Table, file, filter, oligo['o2'], 'reverse')
#
#
# taxTable = buildTaxonomicTable(o1Table)
# speTable = buildSpecificityTable(o1Table)
#
headers = ("oligo", "Num", "LCT Taxid", "Sc Name", "Rank", "distance")
types = (str, int, int, str, str, int)
o1Table = ecoTable(headers, types)
o2Table = ecoTable(headers, types)
buildOligoTable(o1Table, file, filter, oligo['o1'], 'direct')
buildOligoTable(o2Table, file, filter, oligo['o2'], 'reverse')
taxTable = buildTaxonomicTable(o1Table)
speTable = buildSpecificityTable(o1Table)
seqHeaders = ("sequence","taxid")
seqTypes = (str,list)
seqTable = Table(seqHeaders,seqTypes)
#
# seqHeaders = ("sequence","taxid")
# seqTypes = (str,list)
# seqTable = Table(seqHeaders,seqTypes)
return buildSequenceTable(seqTable, file, filter)
return seqTable
return o1Table, o2Table, taxTable