from datasetsToTranscriptList import datasetToListOfTranscripts
path = sys.argv[1]
filenameList = os.listdir(path)
filenames = []
for filename in filenameList:
filenames.append(filename)
filenames.sort()
filenameToDataset = dict()
for filename in filenames:
filenameToDataset[filename] = parser.parseNameToGene(open(path + filename, 'r'))
transcriptList = datasetToListOfTranscripts(filenameToDataset)
graph = dict()
def computeLeastSquaresError(transcriptList, transcriptTupleA, transcriptTupleB):
transcriptsA = transcriptList[transcriptTupleA]
transcriptsB = transcriptList[transcriptTupleB]
lse = 0
for filename in transcriptsA:
transcriptA = transcriptsA[filename]
transcriptB = transcriptsB[filename]
lse += (transcriptA.relativePercent - transcriptB.relativePercent) ** 2
return lse
#!/usr/bin/env python2
import sys
import parser
filename = sys.argv[1]
nameToGene = parser.parseNameToGene(open(filename, 'r'))
geneName = sys.argv[2]
gene = nameToGene[geneName]
print gene
from pylab import *
figure(1, figsize=(6,6))
ax = axes([0.1, 0.1, 0.8, 0.8])
labels = []
percs = []
for transcript in gene.transcripts:
labels.append(transcript.name)
percs.append(transcript.percent*100)
pie(percs, explode=None, labels=labels,
autopct='%1.1f%%', shadow=True, startangle=90)
title(geneName, bbox={'facecolor':'0.8', 'pad':5})