Python Configure.setIdentity Examples

Example #1

# -*- 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()

Example #2

File: test_smartseq2_workflow.py Project: chansigit/zuoye

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)