maggie.rules

import itertools
import os
import collections
import json
import glob
from snakemake.utils import R
#from snakemake.utils import min_vession
#min_version("3.2")
#module load snakemake/3.8.0
from snakemake.exceptions import MissingInputException

#Author:        Rajesh Patidar
#Email:         patidarr
# This will make a output file for every model containing output of bcftools gtcheck

# Snakemake Base location
shell.prefix("""
set -e -o pipefail
module purge
sleep 20s
""")

PATH="/data/MoCha/processedDATA/MAGGIE/"
PAT_FILES = {}

PATIENT ={}
F=sorted(glob.glob(PATH+"*germline*WES*gz"))
for files in F:
	column = files.split("_")
	patient=column[0].split("/")
	PATIENT[patient[5]] =["/data/MoCha/processedDATA/"+patient[5]+"/20170910/qc/"+patient[5]+".maggie.txt"]
	PAT_FILES[patient[5]] =[files]

F=sorted(glob.glob(PATH+"*WES*gz"))
for files in F:
	column = files.split("~")
	patient=column[0].split("/")
	if "_germline" not in patient[5]:
		PATIENT[patient[5]] =["/data/MoCha/processedDATA/"+patient[5]+"/20170910/qc/"+patient[5]+".maggie.txt"]
		if patient[5] not in  PAT_FILES:
			PAT_FILES[patient[5]] =[files]
		
F=sorted(glob.glob(PATH+"*RNASEQ*gz"))
for files in F:
	column = files.split("~")
	patient=column[0].split("/")
	if patient[5] not in  PAT_FILES:
		PATIENT[patient[5]] =["/data/MoCha/processedDATA/"+patient[5]+"/20170910/qc/"+patient[5]+".maggie.txt"]
		PAT_FILES[patient[5]] =[files]

#################################
#localrules: Final
#################################
rule Final:
	input:	PATIENT.values()
#################################
#	This rule will make the Patient Level file
#################################
rule PatientLevel:
	input:
		lambda wildcards: PAT_FILES[wildcards.patient]
	output:
		txt="/data/MoCha/processedDATA/{patient}/20170910/qc/{patient}.maggie.txt",
		pdf="/data/MoCha/processedDATA/{patient}/20170910/qc/{patient}.maggie.pdf"
	params:
		rulename   = "MAGGIE",
	shell:"""
	#################################
	module load samtools/1.2
	echo -e "Model\\tSample\\tScore\\tSites" >{output.txt}
	for file2 in {PATH}/*.codingsynon.sorted.vcf.gz	
		do
			name=`basename ${{file2}} .codingsynon.sorted.vcf.gz`
			name=`echo ${{name}}|sed -e 's/.star//g'|sed -e 's/.bwa//g'`
			score=`bcftools gtcheck -g {input} -G 1 ${{file2}} |grep ^CN |cut -f2,4 |awk '{{OFS="\\t"}}{{print +$1,$2}}'`
			echo -e "{wildcards.patient}\\t${{name}}\\t${{score}}"
		done >>{output.txt}
	module load R
	/data/MoCha/patidarr/ngs_pipeline/scripts/PlotMaggie.R --input={output.txt} --patient={wildcards.patient} --output={output.pdf}
	#################################
	"""