1000RNASEQ chicken ASE: add bai inputs, correct phaser.py commande line

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

@@ -22,11 +22,25 @@ def get_splitNCigar_bam(wildcards):
     else :
     	raise Exception(wildcards.sample + " is sequenced in pair end & single end mode\n 	This workflow do not accept this case!\n")
 
+def get_splitNCigar_bai(wildcards):
+
+    sample_table = table[table["sample_name"] == wildcards.sample]
+    
+    # paired end, filter on properly paired and rmdup
+    if len(sample_table["forward_read"]) == len(sample_table["reverse_read"].dropna()) :
+        return "Results/STAR_Aln_2/" + wildcards.sample + "_rg_genomic_pp_rmdup_uniq_split.bai"
+    # single end, no filter
+    elif len(sample_table["reverse_read"].dropna() ) == 0:
+        return "Results/STAR_Aln_2/" + wildcards.sample + "_rg_genomic_rmdup_uniq_split.bai"
+    else :
+    	raise Exception(wildcards.sample + " is sequenced in pair end & single end mode\n 	This workflow do not accept this case!\n")
+
 rule ASEReadCounter:
 	input:
 		ref = config["fasta_ref"],
 		vcf = 'Results/hard_filtering/' + os.path.basename(config['vcf']).replace('.vcf.gz','') + '_SNP_filtered.vcf.gz',
-		bam = get_splitNCigar_bam
+		bam = get_splitNCigar_bam ,
+		bai = get_splitNCigar_bai 
 	output:
 		cvs = 'Results/Counter/{sample}_ASEReadCounter.csv'
 	log:
@@ -44,7 +58,8 @@ rule ASEReadCounter:
 rule phASER:
 	input:
 		vcf = 'Results/hard_filtering/' + os.path.basename(config['vcf']).replace('.vcf.gz','') + '_SNP_filtered.vcf.gz',
-		bam = get_splitNCigar_bam
+		bam = get_splitNCigar_bam,
+		bai = get_splitNCigar_bai
 	output:
 		cvs = 'Results/Counter/{sample}_phASER.csv'
 	log:
@@ -55,5 +70,5 @@ rule phASER:
    		paired_option = lambda wildcards : '1' if len(table[table['sample_name'] == wildcards.sample]['forward_read']) == len(table[table['sample_name'] == wildcards.sample]['reverse_read'].dropna()) else '0'
 	shell:
 		"""
-		python2.7 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}
+		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}
 		"""