Python MyCEL示例

示例#1

        probe2seq[probe_id] = probe_seq
        coord[(int(probe_coor_x), int(probe_coor_y))] = probe_id

    probeSequenceTabFile.close()

    return probe2seq, coord


celFilePath = sys.argv[1]
celFileName = os.path.basename(celFilePath)
outFilePath = sys.argv[2]
probeSequenceTabFilePath = sys.argv[3]
probeSequenceTabColIndices = [int(x) for x in sys.argv[4].split("/")]
modelProbesFilePath = sys.argv[5]

cel = MyCEL()
norm = Normalize()

if os.path.exists(outFilePath):
    print "Already processed %s" % outFilePath
else:
    print "Reading annotations"
    probe2seq, coord2probe = getMetadata(probeSequenceTabFilePath,
                                         probeSequenceTabColIndices)

    print "Reading " + celFilePath
    probeIntensity = cel.read_cel(celFilePath, coord2probe)

    modelProbes = None
    if os.path.exists(modelProbesFilePath):
        print "Reading model probes file"

示例#2

文件： normalizeAffyArray.py 项目： anyone1985/BCSP

        probe2seq[probe_id] = probe_seq
        coord[(int(probe_coor_x), int(probe_coor_y))] = probe_id

    probeSequenceTabFile.close()

    return probe2seq, coord

celFilePath = sys.argv[1]
celFileName = os.path.basename(celFilePath)
outFilePath = sys.argv[2]
probeSequenceTabFilePath = sys.argv[3]
probeSequenceTabColIndices = [int(x) for x in sys.argv[4].split("/")]
modelProbesFilePath = sys.argv[5]

cel = MyCEL()
norm = Normalize()

if os.path.exists(outFilePath):
    print "Already processed %s" % outFilePath
else:
    print "Reading annotations"
    probe2seq, coord2probe = getMetadata(probeSequenceTabFilePath, probeSequenceTabColIndices)

    print "Reading " + celFilePath
    probeIntensity = cel.read_cel(celFilePath, coord2probe)

    modelProbes = None
    if os.path.exists(modelProbesFilePath):
        print "Reading model probes file"
        modelProbes = utilities.readVectorFromFile(modelProbesFilePath)

示例#3

文件： PrintAffyPlatform.py 项目： srp33/SCAN

import glob,os,sys,time,posix
import utilities
from mycel import MyCEL

celFilePath = sys.argv[1]

cel = MyCEL()

print cel.read_platform(celFilePath)