def run(args):
steps = __STEPS__
args.assay = __ASSAY__
sample = args.sample
outdir_dic = {}
index = 0
for step in steps:
outdir = f"{sample}/{index:02d}.{step}"
outdir_dic.update({step: outdir})
index += 1
step = "sample"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.sample_info import sample_info
sample_info(args)
step = "barcode"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.barcode import barcode
barcode(args)
step = "cutadapt"
args.outdir = f'{outdir_dic[step]}/'
args.fq = f'{outdir_dic["barcode"]}/{sample}_2.fq.gz'
from celescope.tools.cutadapt import cutadapt
cutadapt(args)
step = 'STAR'
args.outdir = f'{outdir_dic[step]}/'
args.fq = f'{outdir_dic["cutadapt"]}/{sample}_clean_2.fq.gz'
from celescope.tools.STAR import STAR
STAR(args)
step = 'featureCounts'
args.outdir = f'{outdir_dic[step]}/'
args.input = f'{outdir_dic["STAR"]}/{sample}_Aligned.sortedByCoord.out.bam'
from celescope.tools.featureCounts import featureCounts
featureCounts(args)
step = 'count'
args.outdir = f'{outdir_dic[step]}/'
args.bam = f'{outdir_dic["featureCounts"]}/{sample}_name_sorted.bam'
from celescope.tools.count import count
count(args)
step = 'analysis'
args.outdir = f'{outdir_dic[step]}/'
args.matrix_file = f'{outdir_dic["count"]}/{sample}_matrix.tsv.gz'
from celescope.tools.analysis import analysis
analysis(args)
def run(args):
steps = __STEPS__
args.assay = __ASSAY__
sample = args.sample
outdir_dic = {}
index = 0
for step in steps:
outdir = f"{sample}/{index:02d}.{step}"
outdir_dic.update({step: outdir})
index += 1
step = "sample"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.sample_info import sample_info
sample_info(args)
step = "barcode"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.barcode import barcode
barcode(args)
step = "cutadapt"
args.outdir = f'{outdir_dic[step]}/'
args.fq = f'{outdir_dic["barcode"]}/{sample}_2.fq.gz'
from celescope.tools.cutadapt import cutadapt
cutadapt(args)
step = 'mapping_smk'
args.SMK_read2 = f'{outdir_dic["cutadapt"]}/{sample}_clean_2.fq.gz'
args.outdir = f'{outdir_dic[step]}/'
from celescope.smk.mapping_smk import mapping_smk
mapping_smk(args)
step = 'count_smk'
args.read_file = f'{outdir_dic["mapping_smk"]}/{sample}_read_count.tsv'
args.outdir = f'{outdir_dic[step]}/'
from celescope.smk.count_smk import count_smk
count_smk(args)
step = 'analysis_smk'
args.tsne_tag_file = f'{outdir_dic["count_smk"]}/{sample}_tsne_tag.tsv'
args.outdir = f'{outdir_dic[step]}/'
from celescope.smk.analysis_smk import analysis_smk
analysis_smk(args)
def run(args):
steps = [
'sample', 'barcode', 'cutadapt', "STAR_virus", "count_capture_virus"
]
sample = args.sample
args.assay = "capture_virus"
outdir_dic = {}
index = 0
for step in steps:
outdir = f"{sample}/{index:02d}.{step}"
outdir_dic.update({step: outdir})
index += 1
step = "sample"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.sample_info import sample_info
sample_info(args)
step = "barcode"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.barcode import barcode
barcode(args)
step = "cutadapt"
args.outdir = f'{outdir_dic[step]}/'
args.fq = f'{outdir_dic["barcode"]}/{sample}_2.fq.gz'
from celescope.tools.cutadapt import cutadapt
cutadapt(args)
step = "STAR_virus"
args.input_read = f'{outdir_dic["cutadapt"]}/{sample}_clean_2.fq.gz'
args.outdir = f'{outdir_dic[step]}/'
from celescope.rna_virus.STAR_virus import STAR_virus
STAR_virus(args)
step = 'count_capture_virus'
args.virus_bam = f'{outdir_dic["STAR_virus"]}/{sample}_virus_Aligned.sortedByCoord.out.bam'
args.outdir = f'{outdir_dic[step]}/'
from celescope.capture_virus.count_capture_virus import count_capture_virus
count_capture_virus(args)
def run(args):
steps = __STEPS__
args.assay = __ASSAY__
sample = args.sample
outdir_dic = {}
index = 0
for step in steps:
outdir = f"{sample}/{index:02d}.{step}"
outdir_dic.update({step: outdir})
index += 1
step = "sample"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.sample_info import sample_info
sample_info(args)
step = "barcode"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.barcode import barcode
barcode(args)
step = "cutadapt"
args.outdir = f'{outdir_dic[step]}/'
args.fq = f'{outdir_dic["barcode"]}/{sample}_2.fq.gz'
from celescope.tools.cutadapt import cutadapt
cutadapt(args)
step = 'mapping_vdj'
args.fq = f'{outdir_dic["cutadapt"]}/{sample}_clean_2.fq.gz'
args.outdir = f'{outdir_dic[step]}/'
from celescope.vdj.mapping_vdj import mapping_vdj
mapping_vdj(args)
step = 'count_vdj'
args.UMI_count_filter1_file = f'{outdir_dic["mapping_vdj"]}/{sample}_UMI_count_filtered1.tsv'
args.outdir = f'{outdir_dic[step]}/'
from celescope.vdj.count_vdj import count_vdj
count_vdj(args)
def run(args):
steps = __STEPS__
args.assay = __ASSAY__
sample = args.sample
outdir_dic = {}
index = 0
for step in steps:
outdir = f"{sample}/{index:02d}.{step}"
outdir_dic.update({step: outdir})
index += 1
step = "sample"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.sample_info import sample_info
sample_info(args)
step = "barcode"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.barcode import barcode
barcode(args)
step = "cutadapt"
args.outdir = f'{outdir_dic[step]}/'
args.fq = f'{outdir_dic["barcode"]}/{sample}_2.fq.gz'
from celescope.tools.cutadapt import cutadapt
cutadapt(args)
step = "STAR_fusion"
args.input_read = f'{outdir_dic["cutadapt"]}/{sample}_clean_2.fq.gz'
args.outdir = f'{outdir_dic[step]}/'
from celescope.fusion.STAR_fusion import STAR_fusion
STAR_fusion(args)
step = 'count_fusion'
args.outdir = f'{outdir_dic[step]}/'
args.bam = f'{outdir_dic["STAR_fusion"]}/{sample}_Aligned.sortedByCoord.out.bam'
from celescope.fusion.count_fusion import count_fusion
count_fusion(args)
def run(args):
steps = ['sample', 'barcode', 'cutadapt', 'STAR', "STAR_virus", "featureCounts", "count", "count_virus",
'analysis']
sample = args.sample
args.assay = "rna_virus"
outdir_dic = {}
index = 0
for step in steps:
outdir = f"{sample}/{index:02d}.{step}"
outdir_dic.update({step: outdir})
index += 1
step = "sample"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.sample_info import sample_info
sample_info(args)
step = "barcode"
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.barcode import barcode
barcode(args)
step = "cutadapt"
args.outdir = f'{outdir_dic[step]}/'
args.fq = f'{outdir_dic["barcode"]}/{sample}_2.fq.gz'
from celescope.tools.cutadapt import cutadapt
cutadapt(args)
step = "STAR"
args.fq = f'{outdir_dic["cutadapt"]}/{sample}_clean_2.fq.gz'
args.outdir = f'{outdir_dic[step]}/'
args.out_unmapped = True
from celescope.tools.STAR import STAR
STAR(args)
step = "STAR_virus"
args.input_read = f'{outdir_dic["STAR"]}/{sample}_Unmapped.out.mate1'
args.outdir = f'{outdir_dic[step]}/'
from celescope.rna_virus.STAR_virus import STAR_virus
STAR_virus(args)
step = 'featureCounts'
args.input = f'{outdir_dic["STAR"]}/{sample}_Aligned.sortedByCoord.out.bam'
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.featureCounts import featureCounts
featureCounts(args)
step = 'count'
args.bam = f'{outdir_dic["featureCounts"]}/{sample}_name_sorted.bam'
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.count import count
count(args)
step = 'count_virus'
args.virus_bam = f'{outdir_dic["STAR_virus"]}/{sample}_virus_Aligned.sortedByCoord.out.bam'
args.barcode_file = f'{outdir_dic["count"]}/matrix_10X/{sample}_cellbarcode.tsv'
args.outdir = f'{outdir_dic[step]}/'
from celescope.virus.count_virus import count_virus
count_virus(args)
step = 'analysis'
args.matrix_file = f'{outdir_dic["count"]}/{sample}_matrix.xls'
args.virus_file = f'{outdir_dic["virus_count"]}/{sample}_virus_UMI_count.tsv'
args.outdir = f'{outdir_dic[step]}/'
from celescope.tools.analysis import analysis
analysis(args)