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():
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_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'))
# TO FINISH AND TEST phaser_expr_matrix
# 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)
# ['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/Summary/Log_TrimGalore_summary.tsv',
# 'Results_ASE/Summary/Log_STAR_Aln_1_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_withGTpopCR50_DPgt05rPopCR20_GT.tsv',
# 'Results_ASE/vcfFiltration/variants_FsQdBiall_withGTpopCR50_DPgt05rPopCR20_DP.tsv',
# 'Results_ASE/vcfFiltration/variants_FsQdBiall_withGTpopCR50_DPgt05rPopCR20_AD.tsv',
# 'Results_ASE/Summary/variants_VariantFiltration_summary.txt',
# 'Results_ASE/Counter/samplePE_ASEReadCounter.csv',
# 'Results_ASE/Counter/samplePE_phASER.allelic_counts.txt',
# 'Results_ASE/Counter/sampleSE_ASEReadCounter.csv',
# 'Results_ASE/Counter/sampleSE_phASER.allelic_counts.txt']
# ['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/Summary/Log_TrimGalore_summary.tsv',
# 'Results_ASE/Summary/Log_STAR_Aln_1_summary.tsv',
# 'Results_ASE/Summary/Log_STAR_Aln_2_summary.tsv',
# 'Results_ASE/vcfFiltration/variants_FsQdBiall.vcf.gz',
# '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_AD.tsv',
# 'Results_ASE/Summary/variants_VariantFiltration_summary.txt',
# 'Results_ASE/ASEReadCounter/samplePE_ASEReadCounter.csv',
# 'Results_ASE/phASER/samplePE_phASER.allelic_counts.txt',
# 'Results_ASE/phASER_gene_ae/samplePE_phASER.gene_ae.txt',
# 'Results_ASE/ASEReadCounter/sampleSE_ASEReadCounter.csv',
# 'Results_ASE/phASER/sampleSE_phASER.allelic_counts.txt',
# 'Results_ASE/phASER_gene_ae/sampleSE_phASER.gene_ae.txt']
rule all:
input:
......
......@@ -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
"""
rule phASER_expr_matrix:
input:
expand("Results_ASE/phASER_gene_ae/{sample}_phASER.gene_ae.txt", sample=table["sample_name"].unique()),
bed = 'Results_ASE/ref_bed/' + os.path.basename(config['gtf_ref']).replace('.gtf', '.bed')
output:
'Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.bed'),
'Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.gw_phased.bed')
params:
gene_ae_dir = "Results_ASE/phASER_gene_ae/",
out_dir = 'Results_ASE/phASER_pop/'
threads: config["phASER_expr_matrix"]["cpu"]
shell:
"""
python2.7 {config[bin_dir]}/phaser_expr_matrix.py --t {threads} --gene_ae_dir {params.gene_ae_dir} --feature {input.bed} --o {param
"""
# TO FINISH AND TEST
# rule phASER_expr_matrix:
# input:
# expand("Results_ASE/phASER_gene_ae/{sample}_phASER.gene_ae.txt", sample=table["sample_name"].unique()),
# bed = 'Results_ASE/ref_bed/' + os.path.basename(config['gtf_ref']).replace('.gtf', '.bed')
# output:
# 'Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.bed'),
# 'Results_ASE/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.gw_phased.bed')
# params:
# gene_ae_dir = "Results_ASE/phASER_gene_ae/",
# out_dir = 'Results_ASE/phASER_pop/'
# threads: config["phASER_expr_matrix"]["cpu"]
# 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