# -*- coding: utf-8 -*- from SamToBam import SamToBam from StepBase import Configure, Schedule Configure.setRefDir('/home/hca/zhangwei1/hg19_bowtie2') Configure.setGenome('hg19') Configure.setIdentity('ATAC') test = SamToBam(samInput='./minidata/atac/SamForTest', threads=5, bamOutputDir='./bamOutputDir') Schedule.run()
from StepBase import Schedule, Configure from FastqDump import FastqDump from Hisat2 import Hisat2 from SamToBam import SamToBam from BamSort import BamSort from Cufflinks import Cufflinks from Cuffmerge import Cuffmerge Configure.setIdentity('sqchen') #Fastq-dump fastq_dump = FastqDump(sraInput1='./minidata/smartseq/sra') # print(fastq_dump.outputs) #Hisat2 hisat = Hisat2(ht2Idx="./minidata/smartseq/hg19_index/genome")(fastq_dump) # print (hisat.outputs) # Bam2Sam # Configure.setRefDir('../../yinqijin/hg19_bowtie2/') # Configure.setGenome('hg19') sam2bam = SamToBam(threads=5)(hisat) # print (sam2bam.outputs) # #BamSort bamsort = BamSort()(sam2bam) # print (bamsort.outputs) # #Cufflinks cufflinks = Cufflinks(gtfInput='./minidata/smartseq/genome.gtf', threads=16)(bamsort)