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Commit 7347a093 authored by Maria Bernard's avatar Maria Bernard
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1000RNASeq ASE : add some changes from initial version uncommit

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...@@ -150,8 +150,12 @@ final_outputs.append('Results/Summary/' + os.path.basename(config['vcf']).replac ...@@ -150,8 +150,12 @@ final_outputs.append('Results/Summary/' + os.path.basename(config['vcf']).replac
# counter # counter
for sample in table["sample_name"].unique(): for sample in table["sample_name"].unique():
final_outputs.append('Results/Counter/' + sample + '_ASEReadCounter.csv') final_outputs.append('Results/ASEReadCounter/' + sample + '_ASEReadCounter.csv')
final_outputs.append('Results/Counter/' + sample + '_phASER.allelic_counts.txt') final_outputs.append('Results/phASER/' + sample + '_phASER.allelic_counts.txt')
final_outputs.append('Results/phASER_gene_ae/' + sample + '_phASER.gene_ae.txt')
final_outputs.append('Results/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.bed'))
final_outputs.append('Results/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.gw_phased.bed'))
# print(final_outputs) # print(final_outputs)
# ['Results/STAR_Aln_2/samplePE_rg_genomic_pp_rmdup_uniq_split.bam', # ['Results/STAR_Aln_2/samplePE_rg_genomic_pp_rmdup_uniq_split.bam',
......
...@@ -37,5 +37,8 @@ SplitNCigarReads : ...@@ -37,5 +37,8 @@ SplitNCigarReads :
phASER: phASER:
mem : "20G" mem : "20G"
phASER_expr_matrix:
cpu : 8
ASEReadCounter: ASEReadCounter:
mem : "20G" mem : "20G"
...@@ -44,7 +44,7 @@ rule ASEReadCounter: ...@@ -44,7 +44,7 @@ rule ASEReadCounter:
bam = get_splitNCigar_bam, bam = get_splitNCigar_bam,
bai = get_splitNCigar_bai bai = get_splitNCigar_bai
output: output:
cvs = 'Results/Counter/{sample}_ASEReadCounter.csv' cvs = 'Results/ASEReadCounter/{sample}_ASEReadCounter.csv'
params: params:
mem = config["ASEReadCounter"]["mem"], mem = config["ASEReadCounter"]["mem"],
mappingQuality = config['mappingQuality'], mappingQuality = config['mappingQuality'],
...@@ -54,6 +54,17 @@ rule ASEReadCounter: ...@@ -54,6 +54,17 @@ rule ASEReadCounter:
gatk --java-options "-Xmx{params.mem}" ASEReadCounter -R {input.ref} -O {output} -I {input.bam} --variant {input.vcf} --min-mapping-quality {params.mappingQuality} --min-base-quality {params.baseQuality} gatk --java-options "-Xmx{params.mem}" ASEReadCounter -R {input.ref} -O {output} -I {input.bam} --variant {input.vcf} --min-mapping-quality {params.mappingQuality} --min-base-quality {params.baseQuality}
""" """
rule gtf2bed:
input:
gtf = config['gtf_ref']
output:
bed = 'Results/ref_bed/' + os.path.basename(config['gtf_ref']).replace('.gtf', '.bed')
script:
"""
../script/gtf2bed.py
"""
rule phASER: rule phASER:
input: input:
vcf = 'Results/vcfFiltration/' + os.path.basename(config['vcf']).replace('.vcf.gz','_FsQdBiall.vcf.gz'), vcf = 'Results/vcfFiltration/' + os.path.basename(config['vcf']).replace('.vcf.gz','_FsQdBiall.vcf.gz'),
...@@ -61,7 +72,8 @@ rule phASER: ...@@ -61,7 +72,8 @@ rule phASER:
bam = get_splitNCigar_bam, bam = get_splitNCigar_bam,
bai = get_splitNCigar_bai bai = get_splitNCigar_bai
output: output:
csv = 'Results/Counter/{sample}_phASER.allelic_counts.txt' csv = 'Results/phASER/{sample}_phASER.allelic_counts.txt',
hap_count = 'Results/phASER/{sample}_phASER.haplotypic_counts.txt'
threads: config["phASER"]["cpu"] threads: config["phASER"]["cpu"]
params: params:
mappingQuality = config['mappingQuality'], mappingQuality = config['mappingQuality'],
...@@ -72,3 +84,32 @@ rule phASER: ...@@ -72,3 +84,32 @@ rule phASER:
""" """
python2.7 {config[bin_dir]}/phaser.py --vcf {input.vcf} --bam {input.bam} --sample {wildcards.sample} --threads {threads} --o Results/Counter/{wildcards.sample}_phASER --paired_end {params.paired_option} --baseq {params.baseQuality} --mapq {params.mappingQuality} --id_separator {params.idSeparator} python2.7 {config[bin_dir]}/phaser.py --vcf {input.vcf} --bam {input.bam} --sample {wildcards.sample} --threads {threads} --o Results/Counter/{wildcards.sample}_phASER --paired_end {params.paired_option} --baseq {params.baseQuality} --mapq {params.mappingQuality} --id_separator {params.idSeparator}
""" """
rule phASER_gene_ae:
input:
hap_count = "Results/phASER/{sample}_phASER.haplotypic_counts.txt",
bed = 'Results/ref_bed/' + os.path.basename(config['gtf_ref']).replace('.gtf', '.bed')
output:
gene_ae = "Results/phASER_gene_ae/{sample}_phASER.gene_ae.txt"
params:
idSeparator = '_' if config['id_separator'] == '' else config['id_separator']
shell:
"""
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/phASER_gene_ae/{sample}_phASER.gene_ae.txt", sample=table["sample_name"].unique()),
bed = 'Results/ref_bed/' + os.path.basename(config['gtf_ref']).replace('.gtf', '.bed')
output:
'Results/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.bed'),
'Results/phASER_pop/' + os.path.basename(config['vcf']).replace('.vcf.gz','_phASER.gw_phased.bed')
params:
gene_ae_dir = "Results/phASER_gene_ae/",
out_dir = 'Results/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
"""
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