SNakemake 1000RNASeq ASE: comment phaser_expr_matrix part

Snakemake/1000RNASeq_chicken/ASE/Snakefile

@@ -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:

Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk

@@ -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
+# 		"""