"""
Pipeline: Read mapping on phased or unphased genomes
12/02/2019
Veronica Mixao, Laia Carrete
CRG (Barcelona)
"""
import argparse
import os
import sys
import configparser
from programs_config import program_path
#Setting the correct path for each program
bwa = program_path("bwa")
picard = program_path("picard")
##############
#### MAIN ####
##############
parser = argparse.ArgumentParser(description="Read mapping on phased or unphased genomes.")
parser.add_argument("-o", "--outdir", dest="outDir", action="store", help="Directory where the data will be stored")
parser.add_argument("-thr", "--threads", dest="threads", default="8", help="Number of threads [8]")
parser.add_argument("-hapA", "--hapA", dest="hapA", action= "store", default="None", help="Haplotype A from reference genome (fasta)")
parser.add_argument("-hapB", "--hapB", dest="hapB", action= "store", default="None", help="Haplotype B from reference genome (fasta)")
parser.add_argument("-ref", "--reference", dest="ref", action= "store", default="None", help="Unphased reference genome (fasta) - Only required if no phased haplotypes are provided")
parser.add_argument("-idA", "--TagName_hapA", dest="tagName_hapA", action="store", default="hapA", help="Tag to be added in the output files relative to hapA [default: hapA]")
parser.add_argument("-idB", "--TagName_hapB", dest="tagName_hapB", action="store", default="hapB", help="Tag to be added in the output files relative to hapB [default: hapB]")
parser.add_argument("-t", "--TagName", dest="tagName", action="store", default="strain", help="Tag to be added in the output files if using a non-phased reference [default: strain] - Only required if no phased haplotypes are provided")
#!/usr/bin/env python
"""
Pipeline: Variant calling on phased or unphased genomes
12/02/2018
Veronica Mixao
CRG (Barcelona)
"""
import argparse
import os
import sys
import configparser
from programs_config import program_path
#Setting the correct path for each program
java = program_path("java")
samtools = program_path("samtools")
picard = program_path("picard")
gatk = program_path("gatk")
freebayes = program_path("freebayes")
bcftools = program_path("bcftools")
vcffilter = program_path("vcffilter")
##############
#### MAIN ####
##############
parser = argparse.ArgumentParser(
description="Variant calling on phased or unphased genomes.")
parser.add_argument("-o",
"--outdir",
#!/usr/bin/env python
"""
Pipeline: Read mapping and variant calling on phased genomes with correction for variants and respective haplotype reconstruction
12/02/2018
Veronica Mixao
CRG (Barcelona)
"""
import argparse
import os
import sys
import configparser
from programs_config import program_path
#Setting the correct path for each program
haplotypo = program_path("haplotypo")
if program_path("python") == None:
sys.exit("ERROR!! Please revise the Python path parameters!")
python_path = program_path("python")
##############
#### MAIN ####
##############
parser = argparse.ArgumentParser(
description=
"Read mapping and variant calling on phased genomes with correction for variants and haplotype reconstruction."
)
parser.add_argument("-v",
"--version",
dest="version",