Skip to content
Snippets Groups Projects
Commit 17359c00 authored by Maria Bernard's avatar Maria Bernard
Browse files

SNakemake 1000RNASeq ASE: comment phaser_expr_matrix part

parent e493d0c6
No related branches found
No related tags found
No related merge requests found
...@@ -154,25 +154,28 @@ for sample in table["sample_name"].unique(): ...@@ -154,25 +154,28 @@ for sample in table["sample_name"].unique():
final_outputs.append('Results_ASE/phASER/' + sample + '_phASER.allelic_counts.txt') final_outputs.append('Results_ASE/phASER/' + sample + '_phASER.allelic_counts.txt')
final_outputs.append('Results_ASE/phASER_gene_ae/' + sample + '_phASER.gene_ae.txt') final_outputs.append('Results_ASE/phASER_gene_ae/' + sample + '_phASER.gene_ae.txt')
final_outputs.append('Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.bed')) # TO FINISH AND TEST phaser_expr_matrix
final_outputs.append('Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.gw_phased.bed')) # final_outputs.append('Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.bed'))
# final_outputs.append('Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.gw_phased.bed'))
# print(final_outputs) # print(final_outputs)
# ['Results_ASE/STAR_Aln_2/samplePE_rg_genomic_pp_rmdup_uniq_split.bam', # ['Results_ASE/STAR_Aln_2/samplePE_rg_genomic_pp_rmdup_uniq_split.bam',
# 'Results_ASE/STAR_Aln_2/sampleSE_rg_genomic_rmdup_uniq_split.bam', # 'Results_ASE/STAR_Aln_2/sampleSE_rg_genomic_rmdup_uniq_split.bam',
# 'Results_ASE/Summary/Log_TrimGalore_summary.tsv', # 'Results_ASE/Summary/Log_TrimGalore_summary.tsv',
# 'Results_ASE/Summary/Log_STAR_Aln_1_summary.tsv', # 'Results_ASE/Summary/Log_STAR_Aln_1_summary.tsv',
# 'Results_ASE/Summary/Log_STAR_Aln_2_summary.tsv', # 'Results_ASE/Summary/Log_STAR_Aln_2_summary.tsv',
# 'Results_ASE/Summary/VariantFiltration_summary.txt', # 'Results_ASE/vcfFiltration/variants_FsQdBiall.vcf.gz',
# 'Results_ASE/vcfFiltration/variants_FsQdBiall.vcf.gz', # 'Results_ASE/vcfFiltration/variants_FsQdBiall_withGTpopCR50_DPgt05rPopCR20_GT.tsv',
# 'Results_ASE/vcfFiltration/variants_FsQdBiall_withGTpopCR50_DPgt05rPopCR20_GT.tsv', # 'Results_ASE/vcfFiltration/variants_FsQdBiall_withGTpopCR50_DPgt05rPopCR20_DP.tsv',
# 'Results_ASE/vcfFiltration/variants_FsQdBiall_withGTpopCR50_DPgt05rPopCR20_DP.tsv', # 'Results_ASE/vcfFiltration/variants_FsQdBiall_withGTpopCR50_DPgt05rPopCR20_AD.tsv',
# 'Results_ASE/vcfFiltration/variants_FsQdBiall_withGTpopCR50_DPgt05rPopCR20_AD.tsv', # 'Results_ASE/Summary/variants_VariantFiltration_summary.txt',
# 'Results_ASE/Summary/variants_VariantFiltration_summary.txt', # 'Results_ASE/ASEReadCounter/samplePE_ASEReadCounter.csv',
# 'Results_ASE/Counter/samplePE_ASEReadCounter.csv', # 'Results_ASE/phASER/samplePE_phASER.allelic_counts.txt',
# 'Results_ASE/Counter/samplePE_phASER.allelic_counts.txt', # 'Results_ASE/phASER_gene_ae/samplePE_phASER.gene_ae.txt',
# 'Results_ASE/Counter/sampleSE_ASEReadCounter.csv', # 'Results_ASE/ASEReadCounter/sampleSE_ASEReadCounter.csv',
# 'Results_ASE/Counter/sampleSE_phASER.allelic_counts.txt'] # 'Results_ASE/phASER/sampleSE_phASER.allelic_counts.txt',
# 'Results_ASE/phASER_gene_ae/sampleSE_phASER.gene_ae.txt']
rule all: rule all:
input: input:
......
...@@ -98,18 +98,20 @@ rule phASER_gene_ae: ...@@ -98,18 +98,20 @@ rule phASER_gene_ae:
python2.7 {config[bin_dir]}/phaser_gene_ae.py --haplotypic_counts {input.hap_count} --features {input.bed} --o {output} --id_separa python2.7 {config[bin_dir]}/phaser_gene_ae.py --haplotypic_counts {input.hap_count} --features {input.bed} --o {output} --id_separa
""" """
rule phASER_expr_matrix: # TO FINISH AND TEST
input:
expand("Results_ASE/phASER_gene_ae/{sample}_phASER.gene_ae.txt", sample=table["sample_name"].unique()), # rule phASER_expr_matrix:
bed = 'Results_ASE/ref_bed/' + os.path.basename(config['gtf_ref']).replace('.gtf', '.bed') # input:
output: # expand("Results_ASE/phASER_gene_ae/{sample}_phASER.gene_ae.txt", sample=table["sample_name"].unique()),
'Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.bed'), # bed = 'Results_ASE/ref_bed/' + os.path.basename(config['gtf_ref']).replace('.gtf', '.bed')
'Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.gw_phased.bed') # output:
params: # 'Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.bed'),
gene_ae_dir = "Results_ASE/phASER_gene_ae/", # 'Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.gw_phased.bed')
out_dir = 'Results_ASE/phASER_pop/' # params:
threads: config["phASER_expr_matrix"]["cpu"] # gene_ae_dir = "Results_ASE/phASER_gene_ae/",
shell: # out_dir = 'Results_ASE/phASER_pop/'
""" # threads: config["phASER_expr_matrix"]["cpu"]
python2.7 {config[bin_dir]}/phaser_expr_matrix.py --t {threads} --gene_ae_dir {params.gene_ae_dir} --feature {input.bed} --o {param # shell:
""" # """
# python2.7 {config[bin_dir]}/phaser_expr_matrix.py --t {threads} --gene_ae_dir {params.gene_ae_dir} --feature {input.bed} --o {param
# """
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment