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)