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Snakemake_MethylkitFormat~
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Snakemake_MethylkitFormat~
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"""
Author: V. Rawat
Affiliation: UZH
Aim: A simple Snakemake workflow to convert coverage2cytosine output to Methylkit Input
Date:
Run: snakemake -s <Snakefile>
Version 0.0.2
Latest modification: 15.10.2017
"""
def message(msg):
print (msg)
################################################################################
#localrules:trimming,final
##--------------------------------------------------------------------------------------##
## The list of samples to be processed
##--------------------------------------------------------------------------------------##
SAMPLES, = glob_wildcards("/home/ubuntu/data/5TB/Aphid/20170221.{smp}_R1_val_1.fq.gz_bismark_bt2_pe.deduplicated.bismark.cov")
NB_SAMPLES = len(SAMPLES)
for smp in SAMPLES:
message("Sample " + smp + " will be processed")
### Rule 0
rule final:
input: expand("/home/ubuntu/data/5TB/Aphid/{smp}.MethylKit", smp=SAMPLES)
# input: expand("", smp=SAMPLES)
#Mapping_imputed/BAM/{smp}/20170221.{smp}_R1_val_1.fq.gz_bismark_bt2_pe.bam
### Rule1
rule trimming:
input: "/home/ubuntu/data/5TB/Aphid/20170221.{smp}_R1_val_1.fq.gz_bismark_bt2_pe.deduplicated.bismark.cov"
output: "/home/ubuntu/data/5TB/Aphid/{smp}.MethylKit"
message: """--- Converting....."""
shell: """
awk -F "\\t" '{{coverage = $4+$5;if($3=="+"){ $3 = "F"}; if($3=="-"){ $3 = "R"} if(coverage > 5) {{ meth= ($4*100)/coverage; unmeth =($5*100)/coverage; print $1 "." $2 "\t" $1 "\t" $2 "\t" $3 "\t" coverage "\t" meth "\t" unmeth }}}}' {input} >{output}
"""