import os
import argparse
from RouToolPa.Tools.Filter import FaCut
#from RouToolPa.Tools.Filter import FastQC
from RouToolPa.Routines import FileRoutines
parser = argparse.ArgumentParser()
parser.add_argument("-d",
"--sample_directory",
action="store",
dest="samples_dir",
required=True,
type=lambda s: FileRoutines.check_path(os.path.abspath(s)),
help="Directory with samples")
parser.add_argument(
"-s",
"--samples",
action="store",
dest="samples",
help="Comma-separated list of subdirectories(one per sample) to handle. "
"If not set all subdirectories will be considered as containing samples."
"In sample directory should one(in case SE reads) or two(in case PE reads) files."
"Filenames should should contain '_1.fq' or '_1.fastq' for forward(left) reads, "
" '_2.fq' or '_2.fastq' for reverse(right) reads and '.fq' or '.fastq' for SE reads"
)
parser.add_argument(
"-o",
"--output_dir",
dest="indel_ReadPosRankSum",
type=float,
default=-20.0,
help="Indel ReadPosRankSum threshold. Default - -20.0")
#parser.add_argument("--indel_InbreedingCoeff", action="store", dest="indel_InbreedingCoeff", type=float, default=-0.8,
# help="Indel InbreedingCoeff threshold. Default - -0.8")
parser.add_argument("--indel_FS",
action="store",
dest="indel_FS",
type=float,
default=200.0,
help="Indel FS threshold. Default - 200.0")
args = parser.parse_args()
VariantFiltration.jar_path = FileRoutines.check_path(args.gatk_dir)
VariantFiltration.filter_bad_variants(
args.reference,
args.input_vcf,
args.output_prefix,
snp_filter_name=args.snp_filter_name,
snp_QD=args.snp_QD,
snp_FS=args.snp_FS,
snp_MQ=args.snp_MQ,
#snp_HaplotypeScore=args.snp_HaplotypeScore,
snp_MappingQualityRankSum=args.snp_MappingQualityRankSum,
snp_ReadPosRankSum=args.snp_ReadPosRankSum,
indel_filter_name=args.indel_filter_name,
indel_QD=args.indel_QD,
indel_ReadPosRankSum=args.indel_ReadPosRankSum,
white_list = IdList()
if args.black_list_file:
black_list.read(args.black_list_file)
if args.white_list_file:
white_list.read(args.white_list_file)
out_fd = open(args.cafe_file, "w")
filtered_fd = open("%sfiltered_families.cafe" % args.filtered_family_dir, "w")
out_fd.write("FAMILYDESC\tFAMILY\t%s\n" % ("\t".join(species_list)))
filtered_fd.write("FAMILYDESC\tFAMILY\t%s\n" % ("\t".join(species_list)))
species_filtered_fd_list = OrderedDict()
fam_count_dict = TwoLvlDict()
species_family_dict = TwoLvlDict()
for species in args.species_set:
species_family_dict[species] = SynDict()
species_family_dict[species].read(
"%s%s%s" % (FileRoutines.check_path(args.input), species, args.suffix),
split_values=True,
values_separator=",",
separator="\t")
#print species_family_dict[species]
fam_count_dict[species] = species_family_dict[species].count_synonyms()
#print fam_count_dict[species]
species_filtered_fd_list[species] = open(
"%s%s.fam" % (args.filtered_family_dir, species), "w")
for family in fam_count_dict.sl_keys():
genes_number_list = []
number_of_species = 0
for species in species_list:
genes_number_list.append(fam_count_dict[species][family] if family in
fam_count_dict[species] else 0)
action="store",
dest="max_memory_per_thread",
default="1G",
help="Maximum memory per thread. Default - 1G")
args = parser.parse_args()
if args.prepare_bam and ((not args.prepared_bam_prefix) or
(not args.temp_dir)):
raise ValueError(
"Options -e/--prepared_bam_prefix and -m/--temp_dir must be set if -p/--prepare_bam option is used"
)
SamtoolsV1.threads = args.threads
if args.prepare_bam or args.mix_ends:
FileRoutines.safe_mkdir(FileRoutines.check_path(args.temp_dir))
prepared_pe_bam_file = "%s.bam" % args.prepared_bam_prefix
prepared_unpaired_bam_file = (
"%s.unpaired.bam" %
args.prepared_bam_prefix) if args.mix_ends else None
"""
SamtoolsV1.prepare_bam_for_read_extraction(args.input, args.prepared_bam, temp_file_prefix=args.temp_dir,
max_memory_per_thread=args.max_memory_per_thread)
"""
SamtoolsV1.prepare_bam_for_read_extraction(
args.input,
prepared_pe_bam_file,
temp_file_prefix=args.temp_dir,
max_memory_per_thread=args.max_memory_per_thread,
bam_file_to_write_unpaired_reads=prepared_unpaired_bam_file)
if args.paired:
def snp_call_GATK(alignment,
sample_name,
reference_file,
known_sites_vcf,
stand_emit_conf=40,
stand_call_conf=100,
QD=2.0,
FS=60.0,
MQ=40.0,
HaplotypeScore=13.0,
MappingQualityRankSum=-12.5,
ReadPosRankSum=-8.0,
GATK_dir="",
num_of_threads=5,
skip_base_recalibration=False):
#default filter expression
#"QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0"
gatk_dir = FileRoutines.check_path(GATK_dir)
intermediate_alignment = alignment
if not skip_base_recalibration:
intermediate_alignment = alignment + "_recal_reads.bam"
#Analyze patterns of covariation in the sequence dataset
os.system(
"java -jar %sGenomeAnalysisTK.jar -nct %i -T BaseRecalibrator -R %s -I %s -knownSites %s -o %s_recal_data.table"
% (gatk_dir, num_of_threads, reference_file, alignment,
known_sites_vcf, sample_name))
#Do a second pass to analyze covariation remaining after recalibration
os.system(
"java -jar %sGenomeAnalysisTK.jar -nct %i -T BaseRecalibrator -R %s -I %s -knownSites %s -BQSR %s_recal_data.table -o %s_post_recal_data.table"
% (gatk_dir, num_of_threads, reference_file, alignment,
known_sites_vcf, sample_name, sample_name))
#Generate before/after plots
#os.system("java -jar %sGenomeAnalysisTK.jar -T AnalyzeCovariates -R %s -before %s_recal_data.table -after %s_post_recal_data.table -plots %s_recalibration_plots.pdf"
# % (gatk_dir, reference_file, sample_name, sample_name, sample_name))
#Apply the recalibration to your sequence data
os.system(
"java -jar %sGenomeAnalysisTK.jar -nct %i -T PrintReads -R %s -I %s -BQSR %s_recal_data.table -o %s"
% (gatk_dir, num_of_threads, reference_file, alignment,
sample_name, intermediate_alignment))
print("\nSNP call...\n")
#SNP call
os.system(
" java -jar %sGenomeAnalysisTK.jar -nt %i -l INFO -R %s -T UnifiedGenotyper -I %s -stand_call_conf %i -stand_emit_conf %i -o %s_GATK_raw.vcf --output_mode EMIT_VARIANTS_ONLY"
% (gatk_dir, num_of_threads, reference_file, intermediate_alignment,
stand_call_conf, stand_emit_conf, sample_name))
#extract SNP
os.system(
"java -jar %sGenomeAnalysisTK.jar -T SelectVariants -R %s -V %s_GATK_raw.vcf -selectType SNP -o %s_GATK_raw_no_indel.vcf"
% (gatk_dir, reference_file, sample_name, sample_name))
#extract indels
os.system(
"java -jar %sGenomeAnalysisTK.jar -T SelectVariants -R %s -V %s_GATK_raw.vcf -selectType INDEL -o %s_GATK_raw_only_indel.vcf"
% (gatk_dir, reference_file, sample_name, sample_name))
#filtering
print("\nFiltering SNP...\n")
os.system(
"java -jar %sGenomeAnalysisTK.jar -T VariantFiltration -R %s -V %s_GATK_raw_no_indel.vcf --filterExpression 'QD < %f || FS > %f || MQ < %f || HaplotypeScore > %f || MappingQualityRankSum < %f || ReadPosRankSum < %f' --filterName 'ambigious_snp' -o %s_GATK_filtered_snps.vcf "
% (gatk_dir, reference_file, sample_name, QD, FS, MQ, HaplotypeScore,
MappingQualityRankSum, ReadPosRankSum, sample_name))
#os.system("vcftools --vcf %s_GATK_filtered_snps.vcf --remove-filtered-all --out %s_GATK_best_snps.vcf --recode --recode-INFO-all"
# % (sample_name, sample_name ))
"""
#!/usr/bin/env python
__author__ = 'Sergei F. Kliver'
import argparse
from RouToolPa.Tools.GATK import SelectVariants
from RouToolPa.Routines import FileRoutines
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input_vcf", action="store", dest="input_vcf", required=True,
help="Input vcf file")
parser.add_argument("-o", "--output_vcf", action="store", dest="output_vcf", required=True,
help="Output vcf file")
parser.add_argument("-r", "--reference", action="store", dest="reference", required=True,
help="Fasta with reference genome")
parser.add_argument("-g", "--gatk_directory", action="store", dest="gatk_dir", default="",
help="Directory with GATK jar")
args = parser.parse_args()
SelectVariants.jar_path = FileRoutines.check_path(args.gatk_dir)
SelectVariants.remove_entries_with_filters(args.reference, args.input_vcf, args.output_vcf)