# -*- coding: utf-8 -*-
"""
@Time : 2018/3/29 15:01
@Author : Weizhang
@FileName: test_LibComplexity.py
"""
from hcacn.steps import LibComplexity
from hcacn.core import Configure, Schedule
Configure.setRefDir('/data8t_1/hca/ref/hg19_bowtie2')
Configure.setGenome('hg19')
Configure.setIdentity('ATAC')
lcpx = LibComplexity(bamInput='./minidata/atac/BamForTest')
Schedule.run()
from hcacn.steps import Cufflinks
from hcacn.core import Configure,Schedule
import os
Configure.setRefDir(os.path.join(os.path.expanduser('~'),'songshaoming/ref'))
Configure.setGenome('hg19')
cflk = Cufflinks(bamInput=['./minidata/accepted_hits.bam'],
gtfInput=['./minidata/genome.gtf'],
outputDir=['./']
)
Schedule.run()
from hcacn.steps import Cuffnorm
from hcacn.core import Configure, Schedule
import os
Configure.setRefDir('ref')
Configure.setGenome('hg19')
cfnm = Cuffnorm(
outputdir='./',
markerInput='Cuffquant.0.suffix',
gtfInput='./minidata/genome.gtf',
cxbInput='/data/songshaoming/qat_results/Cuffquant.0.suffix/abundances.cxb'
)
Schedule.run()
from hcacn.steps import Bowtie2
from hcacn.steps import AdapterRemoval
from hcacn.core import Configure, Schedule
import os
Configure.setRefDir('/home/wzhang/genome/hg19_bowtie2/')
Configure.setGenome('hg19')
#Configure.setIdentity('zwei')
Configure.enableDocker(False)
rs = Bowtie2(fastqInput1='./minidata/atac/end1',
fastqInput2='./minidata/atac/end2')
Schedule.run()