from hcacn.steps import EasyTreat from hcacn.core import Configure, Schedule import os #Configure.enableDocker(False) Configure.setIdentity('cyliu') pt = EasyTreat( dgeInput='./step_13_DigitalExpression/out_gene_exon_tagged.dge.txt.gz') Schedule.run()
# -*- coding: utf-8 -*- """ @author: Zhenyi Wang """ from hcacn.core import Configure, Schedule from hcacn.steps import Deseq2 Configure.setIdentity('zywang') Deseq2(matrixdata = "./minidata/Deseq2/Deseq2testdata.txt", annotation = "./minidata/Deseq2/condition.csv", outputpath = None) Schedule.run()
# -*- 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 TrimPolyA from hcacn.steps import BamToFastq from hcacn.steps import StarAlign from hcacn.steps import SortBam from hcacn.steps import MergeBamAlign from hcacn.steps import TagGene from hcacn.steps import DetectError from hcacn.steps import DigitalExpression from hcacn.steps import EasyTreat from hcacn.steps import MonocleQC from hcacn.steps import Monocle_dimreduce_cluster from hcacn.core import Configure, Schedule import os #Configure.enableDocker(False) Configure.setIdentity('lcy2') f2b = FastqToBam(fastqInput1='./minidata/dropseq/read1', fastqInput2='./minidata/dropseq/read2') #fastqInput1 = '../data/hgmm_100/read1', fastqInput2 = '../data/hgmm_100/read2') bm = BamMerge()(f2b) tbc = TagBarcode(baseStart=1, baseEnd=16, baseQuality=10, barcodeRead=1, discardRead=False, tagName='XC', numBaseBelowQuality=1)(bm) tbm = TagBarcode(baseStart=17, baseEnd=26, baseQuality=10,
from hcacn.core import Schedule, Configure from hcacn.steps import FastqDump from hcacn.steps import Hisat2 from hcacn.steps import Tophat2 from hcacn.steps import SamToBam from hcacn.steps import BamSort from hcacn.steps import Cufflinks from hcacn.steps import Cuffmerge from hcacn.steps import Cuffquant from hcacn.steps import Cuffdiff from hcacn.steps import FastQC from hcacn.steps import Stringtie Configure.setIdentity('sqchen32') Configure.setThreads(16) def smartseq_flow(sraInput, ht2Idx_ref, gtf_ref, fa_ref, threads): fastq_dump = FastqDump(sraInput1=sraInput) hisat = Hisat2(ht2Idx=ht2Idx_ref)(fastq_dump) sam2bam = SamToBam()(hisat) bamsort = BamSort()(sam2bam) cufflinks = Cufflinks(gtfInput=gtf_ref)(bamsort) cuffmerge = Cuffmerge(faInput=fa_ref, gtfInput=gtf_ref)(cufflinks) cuffquant = Cuffquant()(bamsort, cuffmerge) cuffdiff = Cuffdiff(faInput=fa_ref)(cuffmerge, cuffquant) Schedule.run() def smartseq_flow2(sraInput, ht2Idx_ref, gtf_ref, fa_ref, threads): fastq_dump = FastqDump(sraInput1=sraInput)
# -*- coding: utf-8 -*- """ @author: Zhenyi Wang 2018/3/29 """ from hcacn.core import Configure, Schedule from hcacn.flows import MatrixPreprocess Configure.setIdentity('MatrixPreprocessflowtest') matObj = MatrixPreprocess(matrixdata="./minidata/matrixRW/matrix.txt", outputpath=None)()
# -*- coding: utf-8 -*- from hcacn.core import Configure, Schedule from hcacn.steps import SingleCellExperiment, SC3_DE, SC3_Cluster #Configure.setRefDir('/data8t_1/hca/ref/hg19_bowtie2') #Configure.setGenome('hg19') Configure.setIdentity('yinqijin') # test single input file # stf = SingleCellExperiment(matrix_file='/data8t_1/hca/zuoye/minidata/downstream/matrix/matrix.csv', # ann_file = '/data8t_1/hca/zuoye/minidata/downstream/annotation/annotation.csv', # matrix_format = 'ORIGIN', # #outputpath = None, # ) # test multi input file and setting output folder sce = SingleCellExperiment( matrix_file='/data8t_1/hca/zuoye/minidata/downstream/matrix/', ann_file='/data8t_1/hca/zuoye/minidata/downstream/annotation/', matrix_format='ORIGIN', outputpath='step_my', ) sc3_de = SC3_DE( outputpath=None, cluster_num=4, )(sce) sc3_cluster = SC3_Cluster( outputpath="./step_my_sc3_cluster",
from hcacn.steps import Cellranger from hcacn.steps import Seuratpreprocessing from hcacn.steps import Seuratrun from hcacn.core import Configure, Schedule Configure.setIdentity('fengchen') test = Cellranger( fastqInput='/home/hca/fengchen/data/10Xdata/fastqs/', refile= '/home/hca/fengchen/data/10Xdata/refdata-cellranger-hg19_and_mm10-1.2.0', expectcells=100) test2 = Seuratpreprocessing( rscript='/home/hca/fengchen/zuoye/Seuratpreprocessing.R')(test) test3 = Seuratrun(rscript='/home/hca/fengchen/zuoye/Seuratrun.R')(test2) Schedule.run() print('')
# coding: utf-8 from hcacn.core import Step,Configure,Schedule from hcacn.steps import FastQC Configure.setIdentity("yinqijin") Configure.enableDocker(True) # Folder Test # fastqc = FastQC('./minidata/test_fastqc/','fastq',) # FileTest #fastqc = FastQC('./minidata/smartseq/fastq/','fastq',) fastqc = FastQC('./minidata/smartseq/fastq/',) Schedule.run()
#!/usr/bin/env python # -*- coding: utf-8 -*- # @Date : 2018-04-07 10:27:03 # @Author : Zhenyi Wang # @Email: [email protected] from hcacn.core import Configure, Schedule from hcacn.flows import Cluster Configure.setIdentity('Clustertest') #test monocle clusterObj = Cluster( matrixdata="./minidata/Monocle/out_gene_exon_tagged.dge.txt", algorithm='Monocle', resultDir='./result')() #test sc3 #ClusterObj= Cluster(sc3matrix_file = "./minidata/sc3cluster/", # sc3ann = './minidata/sc3annotation/', # algorithm = 'sc3', resultDir='./result')()
# -*- coding: utf-8 -*- from hcacn.core import Configure, Schedule from hcacn.flows import FlowExample Configure.setIdentity('weizheng1') rs = FlowExample(fastqInput1='./minidata/atac/end1', fastqInput2='./minidata/atac/end2', refdir='/data8t_1/hca/ref/hg19_bowtie2', genome='hg19', threads=4, resultDir='result')()
import sys sys.path.append("/data8t_1/chenshengquan/zuoye") from hcacn.core import Configure, Schedule from hcacn.flows import FlowSmartseq Configure.setIdentity('sqchen_f6') ### cuffquant # rs=FlowSmartseq(sraInput='/data8t_1/chenshengquan/minidata/test_sra',alignMethod='hisat2', refdir='/data8t_1/ref/smartseq',genome='hg19',threads=16,resultDir='./resultFlowSmartseq_1')() # rs=FlowSmartseq(sraInput='/data8t_1/chenshengquan/minidata/test_sra', alignMethod='tophat2', refdir='/data8t_1/ref/smartseq',genome='hg19',threads=16,resultDir='./resultFlowSmartseq_tophat2')() ### fastq input # rs=FlowSmartseq(fastqInput1='/data8t_1/chenshengquan/minidata/test_fastq1', fastqInput2='/data8t_1/chenshengquan/minidata/test_fastq2', alignMethod='hisat2', refdir='/data8t_1/ref/smartseq',genome='hg19',threads=16,resultDir='./resultFlowSmartseq_Hisat2_fastq')() ### HTSeq # rs=FlowSmartseq(sraInput='/data8t_1/chenshengquan/minidata/test_sra',alignMethod='hisat2', refdir='/data8t_1/ref/smartseq',genome='hg19',threads=16,resultType='htseq', resultDir='./resultFlowSmartseq_Hisat2_htseq')() ### fastq input rs = FlowSmartseq(fastqInput1='/data8t_1/chenshengquan/minidata/test_fastq1', fastqInput2='/data8t_1/chenshengquan/minidata/test_fastq2', alignMethod='hisat2', refdir='/data8t_1/ref/smartseq', genome='hg19', threads=16, resultType='htseq', resultDir='./resultFlowSmartseq_Hisat2_fastq_htseq')()