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Commit d18d5994 authored by BIOPZ-Gypas Foivos's avatar BIOPZ-Gypas Foivos
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Creation of bed file for the CDS coordinates

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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
#################################################################################
......
......@@ -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")
......
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