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covidma.py
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#!/usr/bin/env python
# Standard library imports
import os
import sys
import re
import logging
import concurrent.futures
# Third party imports
import argparse
import subprocess
import datetime
# Local application imports
from misc import check_file_exists, extract_sample, check_create_dir, execute_subprocess, \
extract_read_list, file_to_list, obtain_group_cov_stats, clean_unwanted_files, \
check_reanalysis, vcf_stats, remove_low_quality, obtain_overal_stats
from preprocessing import fastqc_quality, fastp_trimming, format_html_image
from pe_mapper import bwa_mapping, sam_to_index_bam
from bam_variant import picard_dictionary, samtools_faidx, picard_markdup, ivar_trim, ivar_variants, ivar_consensus, \
replace_consensus_header, create_bamstat, create_coverage, create_consensus
from vcf_process import filter_tsv_variants
from annotation import annotate_snpeff, annotate_pangolin, user_annotation, user_annotation_aa, annotation_to_html, \
report_samples_html
from compare_snp import ddtb_add, ddtb_compare, ddbb_create_intermediate, revised_df, remove_position_range
"""
=============================================================
HEADER
=============================================================
INSTITUTION:IiSGM
AUTHOR: Pedro J. Sola (pedroscampoy@gmail.com)
d^v^b
VERSION=0.1
CREATED: 22 Sep 2020
REVISION:
TODO:
Adapt check_reanalysis
Check file with multiple arguments
Check program is installed (dependencies)
================================================================
END_OF_HEADER
================================================================
"""
# COLORS AND AND FORMATTING
END_FORMATTING = '\033[0m'
WHITE_BG = '\033[0;30;47m'
BOLD = '\033[1m'
UNDERLINE = '\033[4m'
RED = '\033[31m'
GREEN = '\033[32m'
MAGENTA = '\033[35m'
BLUE = '\033[34m'
CYAN = '\033[36m'
YELLOW = '\033[93m'
DIM = '\033[2m'
logger = logging.getLogger()
def main():
"""
Create main function to capture code errors: https://stackoverflow.com/questions/6234405/logging-uncaught-exceptions-in-python
"""
# ARGUMENTS
def get_arguments():
parser = argparse.ArgumentParser(
prog='covidma.py', description='Pipeline to call variants (SNVs) with any non model organism. Specialised in SARS-CoV-2')
input_group = parser.add_argument_group('Input', 'Input parameters')
input_group.add_argument('-i', '--input', dest="input_dir", metavar="input_directory",
type=str, required=True, help='REQUIRED.Input directory containing all fast[aq] files')
input_group.add_argument('-r', '--reference', metavar="reference",
type=str, required=True, help='REQUIRED. File to map against')
input_group.add_argument('-a', '--annotation', metavar="annotation",
type=str, required=True, help='REQUIRED. gff3 file to annotate variants')
input_group.add_argument('-s', '--sample', metavar="sample", type=str,
required=False, help='Sample to identify further files')
input_group.add_argument('-L', '--sample_list', type=str, required=False,
help='Sample names to analyse only in the file supplied')
input_group.add_argument('-p', '--primers', type=str, default='/home/laura/DATABASES/Anotacion/COVID/primers/nCoV-2019.bed',
required=False, help='Bed file including primers to trim')
quality_group = parser.add_argument_group(
'Quality parameters', 'parameters for diferent triming conditions')
quality_group.add_argument('-c', '--coverage20', type=int, default=90, required=False,
help='Minimum percentage of coverage at 20x to clasify as uncovered (Default 90)')
quality_group.add_argument('-n', '--min_snp', type=int, required=False,
default=1, help='SNP number to pass quality threshold')
output_group = parser.add_argument_group(
'Output', 'Required parameter to output results')
output_group.add_argument('-o', '--output', type=str, required=True,
help='REQUIRED. Output directory to extract all results')
output_group.add_argument('-C', '--noclean', required=False,
action='store_false', help='Clean unwanted files for standard execution')
params_group = parser.add_argument_group(
'Parameters', 'parameters for diferent stringent conditions')
params_group.add_argument('-T', '--threads', type=str, dest="threads",
required=False, default=16, help='Threads to use')
params_group.add_argument('-M', '--memory', type=str, dest="memory",
required=False, default=32, help='Max memory to use')
annot_group = parser.add_argument_group(
'Annotation', 'parameters for variant annotation')
annot_group.add_argument('-B', '--annot_bed', type=str, default=[],
required=False, action='append', help='bed file to annotate')
annot_group.add_argument('-V', '--annot_vcf', type=str, default=[],
required=False, action='append', help='vcf file to annotate')
annot_group.add_argument('-A', '--annot_aa', type=str, default=[],
required=False, action='append', help='aminoacid file to annotate')
annot_group.add_argument('-R', '--remove_bed', type=str, default=False,
required=False, help='BED file with positions to remove')
annot_group.add_argument('--mash_database', type=str, required=False,
default=False, help='MASH ncbi annotation containing all species database')
annot_group.add_argument('--snpeff_database', type=str, required=False,
default='NC_045512.2', help='snpEFF annotation database')
compare_group = parser.add_argument_group(
'Compare', 'parameters for compare_snp')
compare_group.add_argument('-S', '--only_snp', required=False,
action='store_true', help='Use INDELS while comparing')
arguments = parser.parse_args()
return arguments
args = get_arguments()
######################################################################
#####################START PIPELINE###################################
######################################################################
output = os.path.abspath(args.output)
group_name = output.split("/")[-1]
reference = os.path.abspath(args.reference)
annotation = os.path.abspath(args.annotation)
# LOGGING
# Create log file with date and time
right_now = str(datetime.datetime.now())
right_now_full = "_".join(right_now.split(" "))
log_filename = group_name + "_" + right_now_full + ".log"
log_folder = os.path.join(output, 'Logs')
check_create_dir(log_folder)
log_full_path = os.path.join(log_folder, log_filename)
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(asctime)s:%(message)s')
file_handler = logging.FileHandler(log_full_path)
file_handler.setLevel(logging.DEBUG)
file_handler.setFormatter(formatter)
stream_handler = logging.StreamHandler()
stream_handler.setLevel(logging.INFO)
# stream_handler.setFormatter(formatter)
logger.addHandler(stream_handler)
logger.addHandler(file_handler)
logger.info("\n\n" + BLUE + BOLD +
"STARTING PIPELINE IN GROUP: " + group_name + END_FORMATTING)
today = str(datetime.date.today())
logger.info("ARGUMENTS:")
logger.info(str(args))
# Obtain all R1 and R2 from folder
r1, r2 = extract_read_list(args.input_dir)
# Check if there are samples to filter out
sample_list_F = []
if args.sample_list == None:
logger.info("\n" + "No samples to filter")
for r1_file, r2_file in zip(r1, r2):
sample = extract_sample(r1_file, r2_file)
sample_list_F.append(sample)
else:
logger.info("samples will be filtered")
sample_list_F = file_to_list(args.sample_list)
new_samples = check_reanalysis(args.output, sample_list_F)
logger.info("\n%d samples will be analysed: %s" %
(len(new_samples), ",".join(new_samples)))
#PREPARE REFERENCE FOR MAPPING + FAI + DICT #########
#####################################################
# picard_dictionary(args)
samtools_faidx(args)
#DECLARE FOLDERS CREATED IN PIPELINE ################
#AND KEY FILES ######################################
#####################################################
# Annotation related parameters
# script_dir = os.path.dirname(os.path.realpath(__file__))
# Output related
out_qc_dir = os.path.join(output, "Quality")
out_qc_pre_dir = os.path.join(out_qc_dir, "raw") # subfolder
out_qc_post_dir = os.path.join(out_qc_dir, "processed") # subfolder
out_trim_dir = os.path.join(output, "Trimmed")
out_map_dir = os.path.join(output, "Bam")
out_variant_dir = os.path.join(output, "Variants")
out_variant_ivar_dir = os.path.join(
out_variant_dir, "ivar_raw") # subfolder
out_filtered_ivar_dir = os.path.join(
out_variant_dir, "ivar_filtered") # subfolder
out_consensus_dir = os.path.join(output, "Consensus")
out_consensus_ivar_dir = os.path.join(
out_consensus_dir, "ivar") # subfolder
out_stats_dir = os.path.join(output, "Stats")
out_stats_bamstats_dir = os.path.join(
out_stats_dir, "Bamstats") # subfolder
out_stats_coverage_dir = os.path.join(
out_stats_dir, "Coverage") # subfolder
out_compare_dir = os.path.join(output, "Compare")
out_annot_dir = os.path.join(output, "Annotation")
out_annot_snpeff_dir = os.path.join(out_annot_dir, "snpeff") # subfolder
out_annot_pangolin_dir = os.path.join(
out_annot_dir, "pangolin") # subfolder
out_annot_user_dir = os.path.join(out_annot_dir, "user") # subfolder
out_annot_user_aa_dir = os.path.join(out_annot_dir, "user_aa") # subfolder
new_sample_number = 0
for r1_file, r2_file in zip(r1, r2):
# EXtract sample name
sample = extract_sample(r1_file, r2_file)
args.sample = sample
if sample in sample_list_F:
sample_number = str(sample_list_F.index(sample) + 1)
sample_total = str(len(sample_list_F))
out_markdup_trimmed_name = sample + ".rg.markdup.trimmed.sorted.bam"
output_markdup_trimmed_file = os.path.join(
out_map_dir, out_markdup_trimmed_name)
if sample in new_samples:
new_sample_number = str(int(new_sample_number) + 1)
new_sample_total = str(len(new_samples))
logger.info("\n" + WHITE_BG + "STARTING SAMPLE: " + sample +
" (" + sample_number + "/" + sample_total + ")" + " (" + new_sample_number + "/" + new_sample_total + ")" + END_FORMATTING)
else:
logger.info("\n" + WHITE_BG + "STARTING SAMPLE: " + sample +
" (" + sample_number + "/" + sample_total + ")" + END_FORMATTING)
if not os.path.isfile(output_markdup_trimmed_file):
args.r1_file = r1_file
args.r2_file = r2_file
##############START PIPELINE#####################
#################################################
# INPUT ARGUMENTS
################
check_file_exists(r1_file)
check_file_exists(r2_file)
args.output = os.path.abspath(args.output)
check_create_dir(args.output)
# QUALITY CHECK in RAW with fastqc
######################################################
check_create_dir(out_qc_dir)
out_qc_raw_name_r1 = (".").join(r1_file.split(
'/')[-1].split('.')[0:-2]) + '_fastqc.html'
out_qc_raw_name_r2 = (".").join(r2_file.split(
'/')[-1].split('.')[0:-2]) + '_fastqc.html'
output_qc_raw_file_r1 = os.path.join(
out_qc_pre_dir, out_qc_raw_name_r1)
output_qc_raw_file_r2 = os.path.join(
out_qc_pre_dir, out_qc_raw_name_r2)
if os.path.isfile(output_qc_raw_file_r1) and os.path.isfile(output_qc_raw_file_r2):
logger.info(YELLOW + DIM + output_qc_raw_file_r1 +
" EXIST\nOmmiting QC for sample " + sample + END_FORMATTING)
else:
logger.info(
GREEN + "Checking quality in sample " + sample + END_FORMATTING)
logger.info("R1: " + r1_file + "\nR2: " + r2_file)
fastqc_quality(r1_file, r2_file,
out_qc_pre_dir, args.threads)
"""
TODO: Human filter
"""
# QUALITY TRIMMING AND ADAPTER REMOVAL WITH fastp
###################################################
out_trim_name_r1 = sample + ".trimmed_R1.fastq.gz"
out_trim_name_r2 = sample + ".trimmed_R2.fastq.gz"
output_trimming_file_r1 = os.path.join(
out_trim_dir, out_trim_name_r1)
output_trimming_file_r2 = os.path.join(
out_trim_dir, out_trim_name_r2)
if os.path.isfile(output_trimming_file_r1) and os.path.isfile(output_trimming_file_r2):
logger.info(YELLOW + DIM + output_trimming_file_r1 +
" EXIST\nOmmiting Trimming for sample " + sample + END_FORMATTING)
else:
logger.info(GREEN + "Trimming sample " +
sample + END_FORMATTING)
fastp_trimming(r1_file, r2_file, sample, out_trim_dir,
threads=args.threads, min_qual=20, window_size=10, min_len=35)
# QUALITY CHECK in TRIMMED with fastqc
######################################################
check_create_dir(out_qc_dir)
out_qc_pos_r1 = sample + ".trimmed_R1_fastqc.html"
out_qc_pos_r2 = sample + ".trimmed_R2_fastqc.html"
output_qc_precessed_file_r1 = os.path.join(
out_qc_post_dir, out_qc_pos_r1)
output_qc_precessed_file_r2 = os.path.join(
out_qc_post_dir, out_qc_pos_r2)
if os.path.isfile(output_qc_precessed_file_r1) and os.path.isfile(output_qc_precessed_file_r2):
logger.info(YELLOW + DIM + output_qc_raw_file_r1 +
" EXIST\nOmmiting QC for sample " + sample + END_FORMATTING)
else:
logger.info(
GREEN + "Checking quality in processed sample " + sample + END_FORMATTING)
logger.info("R1: " + output_trimming_file_r1 +
"\nR2: " + output_trimming_file_r2)
fastqc_quality(
output_trimming_file_r1, output_trimming_file_r2, out_qc_post_dir, args.threads)
# MAPPING WITH BWA - SAM TO SORTED BAM - ADD HEADER SG
#####################################################
out_map_name = sample + ".rg.sorted.bam"
output_map_file = os.path.join(out_map_dir, out_map_name)
if os.path.isfile(output_map_file):
logger.info(YELLOW + DIM + output_map_file +
" EXIST\nOmmiting Mapping for sample " + sample + END_FORMATTING)
else:
logger.info(GREEN + "Mapping sample " +
sample + END_FORMATTING)
logger.info("R1: " + output_trimming_file_r1 + "\nR2: " +
output_trimming_file_r2 + "\nReference: " + reference)
bwa_mapping(output_trimming_file_r1, output_trimming_file_r2,
reference, sample, out_map_dir, threads=args.threads)
sam_to_index_bam(
sample, out_map_dir, output_trimming_file_r1, threads=args.threads)
#MARK DUPLICATES WITH PICARDTOOLS ###################
#####################################################
out_markdup_name = sample + ".rg.markdup.sorted.bam"
output_markdup_file = os.path.join(
out_map_dir, out_markdup_name)
if os.path.isfile(output_markdup_file):
logger.info(YELLOW + DIM + output_markdup_file +
" EXIST\nOmmiting Duplucate Mark for sample " + sample + END_FORMATTING)
else:
logger.info(GREEN + "Marking Dupes in sample " +
sample + END_FORMATTING)
logger.info("Input Bam: " + output_map_file)
picard_markdup(output_map_file)
#TRIM PRIMERS WITH ivar trim ########################
#####################################################
if os.path.isfile(output_markdup_trimmed_file):
logger.info(YELLOW + DIM + output_markdup_trimmed_file +
" EXIST\nOmmiting Duplucate Mark for sample " + sample + END_FORMATTING)
else:
logger.info(
GREEN + "Trimming primers in sample " + sample + END_FORMATTING)
logger.info("Input Bam: " + output_markdup_file)
ivar_trim(output_markdup_file, args.primers, sample,
min_length=30, min_quality=20, sliding_window_width=4)
else:
logger.info(YELLOW + DIM + output_markdup_trimmed_file +
" EXIST\nOmmiting BAM mapping and BAM manipulation in sample " + sample + END_FORMATTING)
########################END OF MAPPING AND BAM MANIPULATION#####################################################################
################################################################################################################################
#VARIANT CALLING WTIH ivar variants##################
#####################################################
check_create_dir(out_variant_dir)
out_ivar_variant_name = sample + ".tsv"
out_ivar_variant_file = os.path.join(
out_variant_ivar_dir, out_ivar_variant_name)
if os.path.isfile(out_ivar_variant_file):
logger.info(YELLOW + DIM + out_ivar_variant_file +
" EXIST\nOmmiting Variant call for sample " + sample + END_FORMATTING)
else:
logger.info(
GREEN + "Calling variants with ivar in sample " + sample + END_FORMATTING)
ivar_variants(reference, output_markdup_trimmed_file, out_variant_dir, sample,
annotation, min_quality=15, min_frequency_threshold=0.01, min_depth=1)
#VARIANT FILTERING ##################################
#####################################################
check_create_dir(out_filtered_ivar_dir)
out_ivar_filtered_file = os.path.join(
out_filtered_ivar_dir, out_ivar_variant_name)
if os.path.isfile(out_ivar_filtered_file):
logger.info(YELLOW + DIM + out_ivar_filtered_file +
" EXIST\nOmmiting Variant filtering for sample " + sample + END_FORMATTING)
else:
logger.info(GREEN + "Filtering variants in sample " +
sample + END_FORMATTING)
filter_tsv_variants(out_ivar_variant_file, out_filtered_ivar_dir, min_frequency=0.7,
min_total_depth=10, min_alt_dp=4, is_pass=True, only_snp=False)
#CREATE CONSENSUS with ivar consensus##################
#######################################################
check_create_dir(out_consensus_dir)
check_create_dir(out_consensus_ivar_dir)
out_ivar_consensus_name = sample + ".fa"
out_ivar_consensus_file = os.path.join(
out_consensus_ivar_dir, out_ivar_consensus_name)
if os.path.isfile(out_ivar_consensus_file):
logger.info(YELLOW + DIM + out_ivar_consensus_file +
" EXIST\nOmmiting Consensus for sample " + sample + END_FORMATTING)
else:
logger.info(
GREEN + "Creating consensus with ivar in sample " + sample + END_FORMATTING)
ivar_consensus(output_markdup_trimmed_file, out_consensus_ivar_dir, sample,
min_quality=20, min_frequency_threshold=0.8, min_depth=20, uncovered_character='N')
logger.info(
GREEN + "Replacing consensus header in " + sample + END_FORMATTING)
replace_consensus_header(out_ivar_consensus_file)
########################CREATE STATS AND QUALITY FILTERS########################################################################
################################################################################################################################
#CREATE Bamstats#######################################
#######################################################
check_create_dir(out_stats_dir)
check_create_dir(out_stats_bamstats_dir)
out_bamstats_name = sample + ".bamstats"
out_bamstats_file = os.path.join(
out_stats_bamstats_dir, out_bamstats_name)
if os.path.isfile(out_bamstats_file):
logger.info(YELLOW + DIM + out_bamstats_file +
" EXIST\nOmmiting Bamstats for sample " + sample + END_FORMATTING)
else:
logger.info(GREEN + "Creating bamstats in sample " +
sample + END_FORMATTING)
create_bamstat(output_markdup_trimmed_file,
out_stats_bamstats_dir, sample, threads=args.threads)
#CREATE Bamstats#######################################
#######################################################
check_create_dir(out_stats_coverage_dir)
out_coverage_name = sample + ".cov"
out_coverage_file = os.path.join(
out_stats_coverage_dir, out_coverage_name)
if os.path.isfile(out_coverage_file):
logger.info(YELLOW + DIM + out_coverage_file +
" EXIST\nOmmiting Bamstats for sample " + sample + END_FORMATTING)
else:
logger.info(GREEN + "Creating coverage in sample " +
sample + END_FORMATTING)
create_coverage(output_markdup_trimmed_file,
out_stats_coverage_dir, sample)
# fastqc OUTPUT FORMAT FOR COMPARISON
######################################################
logger.info(
GREEN + "Creating summary report for quality result " + END_FORMATTING)
# format_html_image(out_qc_dir)
# coverage OUTPUT SUMMARY
######################################################
logger.info(
GREEN + "Creating summary report for coverage result " + END_FORMATTING)
obtain_group_cov_stats(out_stats_coverage_dir, group_name)
# READS and VARIANTS OUTPUT SUMMARY
######################################################
logger.info(GREEN + "Creating overal summary report " + END_FORMATTING)
obtain_overal_stats(output, group_name)
# REMOVE UNCOVERED
##############################################################################################################################
logger.info(GREEN + "Removing low quality samples" + END_FORMATTING)
# remove_low_quality(output, min_percentage_20x=args.coverage20,
# min_hq_snp=args.min_snp, type_remove='Uncovered')
#ANNOTATION WITH SNPEFF, USER INOUT AND PANGOLIN ####
#####################################################
logger.info("\n\n" + BLUE + BOLD + "STARTING ANNOTATION IN GROUP: " +
group_name + END_FORMATTING + "\n")
check_create_dir(out_annot_dir)
check_create_dir(out_annot_snpeff_dir)
check_create_dir(out_annot_pangolin_dir)
# SNPEFF
if args.snpeff_database != False:
# CHANGE FOR RAW/FILTERED ANNOTATION
for root, _, files in os.walk(out_filtered_ivar_dir):
if root == out_filtered_ivar_dir: # CHANGE FOR RAW/FILTERED ANNOTATION
for name in files:
if name.endswith('.tsv'):
sample = name.split('.')[0]
filename = os.path.join(root, name)
out_annot_file = os.path.join(
out_annot_snpeff_dir, sample + ".annot")
if os.path.isfile(out_annot_file):
logger.info(YELLOW + DIM + out_annot_file +
" EXIST\nOmmiting snpEff Annotation for sample " + sample + END_FORMATTING)
else:
logger.info(
GREEN + "Annotating sample with snpEff: " + sample + END_FORMATTING)
output_vcf = os.path.join(
out_annot_snpeff_dir, sample + '.vcf')
annotate_snpeff(
filename, output_vcf, out_annot_file, database=args.snpeff_database)
# USER DEFINED
if not args.annot_bed and not args.annot_vcf:
logger.info(
YELLOW + BOLD + "Ommiting User Annotation, no BED or VCF files supplied" + END_FORMATTING)
else:
check_create_dir(out_annot_user_dir)
# CHANGE FOR RAW/FILTERED ANNOTATION
for root, _, files in os.walk(out_variant_ivar_dir):
if root == out_variant_ivar_dir: # CHANGE FOR RAW/FILTERED ANNOTATION
for name in files:
if name.endswith('.tsv'):
sample = name.split('.')[0]
logger.info(
'User bed/vcf annotation in sample {}'.format(sample))
filename = os.path.join(root, name)
out_annot_file = os.path.join(
out_annot_user_dir, sample + ".tsv")
user_annotation(
filename, out_annot_file, vcf_files=args.annot_vcf, bed_files=args.annot_bed)
# USER AA DEFINED
if not args.annot_aa:
logger.info(
YELLOW + BOLD + "Ommiting User aa Annotation, no AA files supplied" + END_FORMATTING)
else:
check_create_dir(out_annot_user_aa_dir)
for root, _, files in os.walk(out_annot_snpeff_dir):
if root == out_annot_snpeff_dir:
for name in files:
if name.endswith('.annot'):
sample = name.split('.')[0]
logger.info(
'User aa annotation in sample {}'.format(sample))
filename = os.path.join(root, name)
out_annot_aa_file = os.path.join(
out_annot_user_aa_dir, sample + ".tsv")
if os.path.isfile(out_annot_aa_file):
user_annotation_aa(
out_annot_aa_file, out_annot_aa_file, aa_files=args.annot_aa)
else:
user_annotation_aa(
filename, out_annot_aa_file, aa_files=args.annot_aa)
# PANGOLIN
with concurrent.futures.ThreadPoolExecutor(max_workers=args.threads) as executor:
futures_pangolin = []
for root, _, files in os.walk(out_consensus_ivar_dir):
if root == out_consensus_ivar_dir:
for name in files:
if name.endswith('.fa'):
sample = name.split('.')[0]
filename = os.path.join(root, name)
out_pangolin_filename = sample + ".lineage.csv"
out_pangolin_file = os.path.join(
out_annot_pangolin_dir, out_pangolin_filename)
if os.path.isfile(out_pangolin_file):
logger.info(YELLOW + DIM + out_pangolin_file +
" EXIST\nOmmiting Lineage for sample " + sample + END_FORMATTING)
else:
logger.info(
GREEN + "Obtaining Lineage in sample " + sample + END_FORMATTING)
future = executor.submit(
annotate_pangolin, filename, out_annot_pangolin_dir, out_pangolin_filename, threads=args.threads, max_ambig=0.6)
futures_pangolin.append(future)
for future in concurrent.futures.as_completed(futures_pangolin):
logger.info(future.result())
# annotate_pangolin(filename, out_annot_pangolin_dir,
# out_pangolin_filename, threads=args.threads, max_ambig=0.6)
# USER AA TO HTML
annotated_samples = []
logger.info('Adapting annotation to html in {}'.format(group_name))
for root, _, files in os.walk(out_annot_user_aa_dir):
if root == out_annot_user_aa_dir:
for name in files:
if name.endswith('.tsv'):
sample = name.split('.')[0]
annotated_samples.append(sample)
filename = os.path.join(root, name)
annotation_to_html(filename, sample)
annotated_samples = [str(x) for x in annotated_samples]
report_samples_html_all = report_samples_html.replace(
'ALLSAMPLES', ('","').join(annotated_samples)) # NEW
with open(os.path.join(out_annot_user_aa_dir, '00_all_samples.html'), 'w+') as f:
f.write(report_samples_html_all)
# SNP COMPARISON using tsv variant files
######################################################
logger.info("\n\n" + BLUE + BOLD + "STARTING COMPARISON IN GROUP: " +
group_name + END_FORMATTING + "\n")
check_create_dir(out_compare_dir)
folder_compare = today + "_" + group_name
path_compare = os.path.join(out_compare_dir, folder_compare)
check_create_dir(path_compare)
full_path_compare = os.path.join(path_compare, group_name)
# ddtb_add(out_filtered_ivar_dir, full_path_compare)
compare_snp_matrix_recal = full_path_compare + ".revised.final.tsv"
compare_snp_matrix_INDEL = full_path_compare + ".revised_INDEL.final.tsv"
compare_snp_matrix_recal_intermediate = full_path_compare + ".revised_intermediate.tsv"
compare_snp_matrix_INDEL_intermediate = full_path_compare + \
".revised_INDEL_intermediate.tsv"
recalibrated_snp_matrix_intermediate = ddbb_create_intermediate(
out_variant_ivar_dir, out_stats_coverage_dir, min_freq_discard=0.1, min_alt_dp=4, only_snp=args.only_snp)
recalibrated_snp_matrix_intermediate.to_csv(
compare_snp_matrix_recal_intermediate, sep="\t", index=False)
compare_snp_matrix_INDEL_intermediate_df = remove_position_range(
recalibrated_snp_matrix_intermediate)
compare_snp_matrix_INDEL_intermediate_df.to_csv(
compare_snp_matrix_INDEL_intermediate, sep="\t", index=False)
recalibrated_revised_df = revised_df(recalibrated_snp_matrix_intermediate, path_compare, min_freq_include=0.7,
min_threshold_discard_sample=0.07, min_threshold_discard_position=0.4, remove_faulty=True, drop_samples=True, drop_positions=True)
recalibrated_revised_df.to_csv(
compare_snp_matrix_recal, sep="\t", index=False)
recalibrated_revised_INDEL_df = revised_df(compare_snp_matrix_INDEL_intermediate_df, path_compare, min_freq_include=0.7,
min_threshold_discard_sample=0.07, min_threshold_discard_position=0.4, remove_faulty=True, drop_samples=True, drop_positions=True)
recalibrated_revised_INDEL_df.to_csv(
compare_snp_matrix_INDEL, sep="\t", index=False)
ddtb_compare(compare_snp_matrix_recal, distance=0)
ddtb_compare(compare_snp_matrix_INDEL, distance=0, indel=True)
logger.info("\n\n" + MAGENTA + BOLD + "COMPARING FINISHED IN GROUP: " +
group_name + END_FORMATTING + "\n")
#####################CONSENSUS WITH REFINED CALL######
######################################################
logger.info(GREEN + "Creating refined consensus" + END_FORMATTING)
create_consensus(reference, compare_snp_matrix_recal,
out_stats_coverage_dir, out_consensus_dir)
logger.info("\n\n" + MAGENTA + BOLD +
"#####END OF PIPELINE COVID MULTI ANALYSIS#####" + END_FORMATTING + "\n")
if __name__ == '__main__':
try:
main()
except Exception as e:
logger.exception(e)
raise