Creation of bed file for the CDS coordinates

snakemake/prepare_annotation/Snakefile

 configfile: "config.yaml"
 
-localrules: create_output_and_log_directories, create_tab_delimited_CDS_file, finish
+localrules: create_output_and_log_directories, create_tab_delimited_CDS_file, create_bed_CDS_file, finish
 
 #################################################################################
 ### Finish rule
@@ -10,7 +10,7 @@ rule finish:
 	input:
 		idx_other = os.path.join(config["output_dir"], "other_RNAs_sequence.idx"),
 		idx_transcripts = os.path.join(config["output_dir"], "longest_pc_transcript_per_gene.idx"),
-		tsv = os.path.join(config["output_dir"], "transcript_id_gene_id_CDS.tsv")
+		bed = os.path.join(config["output_dir"], "transcript_id_gene_id_CDS.bed")
 
 #################################################################################
 ### Create output and log directories
@@ -115,6 +115,24 @@ rule create_tab_delimited_CDS_file:
 		--fasta {input.transcripts} \
 		--out {output.tsv}) &> {log}"
 
+#################################################################################
+### BED CDS table
+#################################################################################
+
+rule create_bed_CDS_file:
+	input:
+		tsv = os.path.join(config["output_dir"], "transcript_id_gene_id_CDS.tsv")
+	output:
+		bed = os.path.join(config["output_dir"], "transcript_id_gene_id_CDS.bed")
+	params:
+		cluster_log = os.path.join(config["cluster_log"], "create_bed_CDS_file.log")
+	log:
+		os.path.join(config["local_log"], "create_bed_CDS_file.log")
+	# singularity:
+	# 	"docker://zavolab/python_htseq_biopython:3.6.5_0.10.0_1.71"
+	shell:
+		"(tail -n+2 {input.tsv} | awk \'{{print $1 \"\t\" $3-1 \"\t\" $4 \"\t\" $2 }}\' > {output.bed}) &> {log}"
+
 #################################################################################
 ### Generate segemehl index for transcripts
 #################################################################################

snakemake/process_data/Snakefile

@@ -233,7 +233,7 @@ rule remove_multimappers:
 
 rule sam2bam_sort_and_index:
 	input:
-		sam = os.path.join(config["output_dir"], "{sample}/transcripts.mapped.sam")
+		sam = os.path.join(config["output_dir"], "{sample}/transcripts.mapped.unique.sam")
 	output:
 		bam = os.path.join(config["output_dir"], "{sample}/transcripts.mapped.unique.sorted.bam"),
 		bai = os.path.join(config["output_dir"], "{sample}/transcripts.mapped.unique.sorted.bam.bai")