Python main Examples

Example #1

File: post_rsq2mut.py Project: SMC1/JK1

def post_rsq2mut(projDirN, idL=[], server="smc1", dbN="ihlee_test"):
    inDirL = filter(lambda x: os.path.isdir(projDirN + "/" + x), os.listdir(projDirN))
    for inDir in inDirL:
        if idL != [] and inDir not in idL:
            continue
        post_s_rsq2mut(projDirN + "/" + inDir, server=server, dbN=dbN)
    makeDB_mutation_rxsq.main(dbN=dbN)

Example #2

def post_rsq2mut(projDirN, idL=[], server='smc1', dbN='ihlee_test'):
    inDirL = filter(lambda x: os.path.isdir(projDirN + '/' + x),
                    os.listdir(projDirN))
    for inDir in inDirL:
        if idL != [] and inDir not in idL:
            continue
        post_s_rsq2mut(projDirN + '/' + inDir, server=server, dbN=dbN)
    makeDB_mutation_rxsq.main(dbN=dbN)

Example #3

File: post_xsq2mut.py Project: SMC1/JK1

def main(singleFileN, somaticFileN, allFileN, server='smc1', dbN='ircr1'):
	if not os.path.isfile(singleFileN):
		prep_single(singleFileN, server, dbN)
		mymysql.reset_table(tableN='mutation', dataFileN=singleFileN, user=mysetting.mysqlH[server]['user'], passwd=mysetting.mysqlH[server]['passwd'], db=dbN, host=mysetting.mysqlH[server]['host'])

	if not os.path.isfile(somaticFileN):
#		prep_somatic(somaticFileN, server, dbN)
		prep_somatic_new(somaticFileN, server, dbN)
	
	if not os.path.isfile(allFileN):
		prepDB_mutation_normal.main(inTFileName=singleFileN, inNFileName=somaticFileN, geneList=[], outFileN=allFileN)
		load_mutation_all(allFileN, server, dbN)
		makeDB_mutation_rxsq.main(dbN)

Example #4

File: post_xsq2mut.py Project: zhangtongyikai/JK1

def main(singleFileN, somaticFileN, allFileN, server='smc1', dbN='ircr1'):
    if not os.path.isfile(singleFileN):
        prep_single(singleFileN, server, dbN)
        mymysql.reset_table(tableN='mutation',
                            dataFileN=singleFileN,
                            user=mysetting.mysqlH[server]['user'],
                            passwd=mysetting.mysqlH[server]['passwd'],
                            db=dbN,
                            host=mysetting.mysqlH[server]['host'])

    if not os.path.isfile(somaticFileN):
        #		prep_somatic(somaticFileN, server, dbN)
        prep_somatic_new(somaticFileN, server, dbN)

    if not os.path.isfile(allFileN):
        prepDB_mutation_normal.main(inTFileName=singleFileN,
                                    inNFileName=somaticFileN,
                                    geneList=[],
                                    outFileN=allFileN)
        load_mutation_all(allFileN, server, dbN)
        makeDB_mutation_rxsq.main(dbN)