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MetaPro_paths.py
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#This program is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#This program is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#GNU General Public License for more details.
#You should have received a copy of the GNU General Public License
#along with this program. If not, see <https://www.gnu.org/licenses/>.
#April 12, 2021
#-------------------------------------------------------------------------
#MetaPro_paths.py
#This code manages all of the locations of files needed to run MetaPro.
#It also controls the import of the configuration file.
import os
import sys
from datetime import datetime as dt
import math
import time
from configparser import ConfigParser, ExtendedInterpolation
class tool_path_obj:
def value_assignment(self, config, config_section, var_name, default):
value = ""
#print("CONFIG:", config)
if config:
if(config_section in config):
if(var_name in config[config_section]):
value = config[config_section][var_name]
if('"' in value):
value = value.strip('"')
#print("quotes cleaned")
#print(var_name, "found! using:", value)
#time.sleep(1)
print(var_name, "found! using:", value)
if(value == "0"):
print(var_name, "zero-setting detected: using default")
else:
print(var_name, "no inner section found. using default", default)
value = default
else:
print(config_section, "no section found, using default:", default)
value = default
else:
print("no config, using default:", default)
value = default
return value
def check_file_valid(self, file_0):
#checks that a file is there, and larger than 0kb
ok_flag = False
if (os.path.exists(file_0)):
if(os.path.getsize(file_0) > 0):
ok_flag = True
return ok_flag
def check_dmd_valid(self):
#if there's a .dmnd file
#if it's sufficiently big
dir_name = os.path.dirname(self.Prot_DB)
basename = os.path.basename(self.Prot_DB)
print("dir name:", dir_name)
file_name = basename.split(".")[0]
print("file name:", file_name)#, "extension:", extension)
print(self.Prot_DB)
if not(os.path.exists(self.Prot_DB)):
sys.exit("file does not exists")
else:
print(dt.today(), self.Prot_DB, "exists")
dmd_index_path = os.path.join(dir_name, file_name + ".dmnd")
db_size = os.path.getsize(self.Prot_DB)
if(os.path.exists(dmd_index_path)):
if(os.path.getsize(dmd_index_path) >= db_size * 0.9):
print(dt.today(), "DMD index is ok")
#Mar 212, 2023: changed to be an external function because we now make custom DBs after a GA pre-scan
def check_bwa_valid(self, DNA_DB):
print(dt.today(), "BWA DB check:", DNA_DB)
if(os.path.exists(DNA_DB)):
if(os.path.isdir(DNA_DB)):
file_list = os.listdir(DNA_DB)
ok_flag = False
file_count = 0
for item in file_list:
if(item.endswith(".fasta")):
#print("CHECKING:", item)
ext_0 = ".amb"
ext_1 = ".ann"
ext_2 = ".bwt"
ext_3 = ".pac"
ext_4 = ".sa"
file_0 = os.path.join(DNA_DB, item + ext_0)
file_1 = os.path.join(DNA_DB, item + ext_1)
file_2 = os.path.join(DNA_DB, item + ext_2)
file_3 = os.path.join(DNA_DB, item + ext_3)
file_4 = os.path.join(DNA_DB, item + ext_4)
ok_flag = self.check_file_valid(file_0)
ok_flag = self.check_file_valid(file_1)
ok_flag = self.check_file_valid(file_2)
ok_flag = self.check_file_valid(file_3)
ok_flag = self.check_file_valid(file_4)
#print("OK FLAG:", ok_flag)
file_count += 1
if(file_count == 0):
print(dt.today(), "Error: no fasta files found. BWA only accepts .fasta extensions")
sys.exit("empty BWA database")
if(not ok_flag):
sys.exit("BWA database has not been fully indexed. try reindexing the database")
else:
print(dt.today(), "BWA database OK")
self.GA_DB_mode = "multi"
else:
if(self.DNA_DB.endswith(".fasta")):
ext_0 = ".amb"
ext_1 = ".ann"
ext_2 = ".bwt"
ext_3 = ".pac"
ext_4 = ".sa"
file_0 = os.path.join(DNA_DB + ext_0)
file_1 = os.path.join(DNA_DB + ext_1)
file_2 = os.path.join(DNA_DB + ext_2)
file_3 = os.path.join(DNA_DB + ext_3)
file_4 = os.path.join(DNA_DB + ext_4)
ok_flag = self.check_file_valid(file_0)
ok_flag = self.check_file_valid(file_1)
ok_flag = self.check_file_valid(file_2)
ok_flag = self.check_file_valid(file_3)
ok_flag = self.check_file_valid(file_4)
if(not ok_flag):
sys.exit("BWA Database FILE has not been fully indexed. Try reindexing the database")
else:
print(dt.today(), "BWA Database File OK")
self.GA_DB_mode = "single"
else:
sys.exit("Error: no fasta file found. BWA only accepts .fasta extensions")
else:
exit_string = str(dt.today()) + " " + "Error: path does not exist. "+ DNA_DB
sys.exit(exit_string)
#if it's a fastq or fasta
#if it's been indexed (all files present)
def check_blat_valid(self, DNA_DB):
#check that there's at least 1 fasta in the dict
#but truth-be-told, this doesn't do anything, since BWA will use the same DB
print(dt.today(), "BLAT DB check:", DNA_DB)
if(os.path.isdir(DNA_DB)):
file_list = os.listdir(DNA_DB)
ok_flag = False
file_count = 0
for item in file_list:
if(item.endswith(".fasta")):
ok_flag = self.check_file_valid(os.path.join(DNA_DB, item))
file_count += 1
if(file_count == 0):
print(dt.today(), "Error: no fasta file found. BLAT accepts .fasta extensions only")
sys.exit()
if(ok_flag):
print(dt.today(), "BLAT database OK")
self.GA_DB_mode = "multi"
else:
sys.exit("Error with BLAT db. there's an empty fasta file")
else:
if(self.DNA_DB.endswith(".fasta")):
ok_flag = self.check_file_valid(DNA_DB)
if(ok_flag):
print(dt.today(), "BLAT Database file OK")
self.GA_DB_mode = "single"
else:
sys.exit("Error with BLAT DB file. it's empty")
else:
print(dt.today(), "Error: no fasta file found. BLAT accepts .fasta extensions only")
sys.exit()
def __init__ (self, config_path):
print("CHECKING CONFIG")
if config_path:
config = ConfigParser() #change this to ex
config.read(config_path)
print("USING CONFIG", config_path)
else:
print("no config found, defaulting")
config = None
script_path = "/pipeline/Scripts"
tool_path = "/pipeline_tools/"
database_path = "/project/j/jparkin/Lab_Databases/"
custom_database_path = "/pipeline/custom_databases/"
#--------------------------------------------------
# miscellaneous values
BWA_mem_default = 50
BLAT_mem_default = 10 #100MB
DIAMOND_mem_default = 50 #60GB
DETECT_mem_default = 50
Infernal_mem_default = 50
Barrnap_mem_default = 50
repop_mem_default = 50
TA_mem_threshold_default = 50
BWA_pp_mem_default = 50
BLAT_pp_mem_default = 50
DIAMOND_pp_mem_default = 50
GA_final_merge_mem_default = 5
EC_mem_threshold_default = 5
cpu_default = int(math.ceil(os.cpu_count() * 0.75))
rRNA_chunksize_default = 50000
EC_chunksize_default = 50000
GA_chunksize_default = 25000
BWA_mem_footprint_default = 5
BLAT_mem_footprint_default = 5
DMD_mem_footprint_default = 10
BWA_job_limit_default = cpu_default
BLAT_job_limit_default = cpu_default
DIAMOND_job_limit_default = cpu_default
DETECT_job_limit_default = cpu_default
Infernal_job_limit_default = 1000
Barrnap_job_limit_default = 1000
BWA_pp_job_limit_default = cpu_default
BLAT_pp_job_limit_default = cpu_default
DIAMOND_pp_job_limit_default = cpu_default
GA_final_merge_job_limit_default = cpu_default
repop_job_limit_default = 1
TA_job_limit_default = cpu_default
EC_job_limit_default = cpu_default
Centrifuge_job_limit_default = 1
Barrnap_job_delay_default = 5
Infernal_job_delay_default = 5
BWA_job_delay_default = 5
BLAT_job_delay_default = 5
DIAMOND_job_delay_default = 5
DETECT_job_delay_default = 5
BWA_pp_job_delay_default = 5
BLAT_pp_job_delay_default = 5
DIAMOND_pp_job_delay_default = 5
GA_final_merge_job_delay_default = 5
repop_job_delay_default = 10
TA_job_delay_default = 5
EC_job_delay_default = 1
keep_all_default = "yes"
keep_quality_default = "no"
keep_host_default = "no"
keep_repop_default = "no"
keep_vector_default = "no"
keep_assemble_contigs_default = "no"
keep_rRNA_default = "no"
keep_GA_BWA_default = "no"
keep_GA_BLAT_default = "no"
keep_GA_DIAMOND_default = "no"
keep_GA_final_default = "no"
keep_TA_default = "no"
keep_EC_default = "no"
keep_outputs_default = "no"
filter_stringency_default = "high"
BWA_cigar_default = 90
BLAT_identity_default = 85
BLAT_length_default = 0.65
BLAT_score_default = 60
DIAMOND_identity_default = 85
DIAMOND_length_default = 0.65
DIAMOND_score_default = 60
#identity_cutoff= 85
#length_cutoff= 0.65
#score_cutoff= 60
self.target_rank = self.value_assignment(config, "Settings", "target_rank", "genus")
self.adapterremoval_minlength = self.value_assignment(config, "Settings", "AdapterRemoval_minlength", 30)
self.show_unclassified = self.value_assignment(config, "Settings", "Show_unclassified", "No")
self.bypass_log_name = self.value_assignment(config, "Settings", "bypass_log_name", "bypass_log.txt")
self.debug_stop_flag = self.value_assignment(config, "Settings", "debug_stop_flag", "none")
self.num_threads = self.value_assignment(config, "Settings", "num_threads", os.cpu_count())
if(self.num_threads == 0):
self.num_threads = 1
self.taxa_exist_cutoff = self.value_assignment(config, "Settings", "taxa_existence_cutoff", 0.1)
self.DNA_DB_mode = self.value_assignment(config, "Settings", "DNA_DB_mode", "chocophlan") #used to indicate custom DB, or our grouped library
#other setting is "custom"
self.RPKM_cutoff = self.value_assignment(config, "Settings", "RPKM_cutoff", 0.01)
self.BWA_cigar_cutoff = self.value_assignment(config, "Settings", "BWA_cigar_cutoff", BWA_cigar_default)
self.BLAT_identity_cutoff = self.value_assignment(config, "Settings", "BLAT_identity_cutoff", BLAT_identity_default)
self.BLAT_length_cutoff = self.value_assignment(config, "Settings", "BLAT_length_cutoff", BLAT_length_default)
self.BLAT_score_cutoff = self.value_assignment(config, "Settings", "BLAT_score_cutoff", BLAT_score_default)
self.DIAMOND_identity_cutoff = self.value_assignment(config, "Settings", "DIAMOND_identity_cutoff", DIAMOND_identity_default)
self.DIAMOND_length_cutoff = self.value_assignment(config, "Settings", "DIAMOND_length_cutoff", DIAMOND_length_default)
self.DIAMOND_score_cutoff = self.value_assignment(config, "Settings", "DIAMOND_score_cutoff", DIAMOND_score_default)
#-----------------------------------------------------------------------------------------------
self.BWA_mem_footprint = self.value_assignment(config, "Settings", "BWA_mem_footprint", BWA_mem_footprint_default)
self.BLAT_mem_footprint = self.value_assignment(config, "Settings", "BLAT_mem_footprint", BLAT_mem_footprint_default)
self.DMD_mem_footprint = self.value_assignment(config, "Settings", "DMD_mem_footprint", DMD_mem_footprint_default)
#-------------------------------------------------------------------------------------------------
self.BWA_mem_threshold = self.value_assignment(config, "Settings", "BWA_mem_threshold", BWA_mem_default)
self.BLAT_mem_threshold = self.value_assignment(config, "Settings", "BLAT_mem_threshold", BLAT_mem_default)
self.DIAMOND_mem_threshold = self.value_assignment(config, "Settings", "DIAMOND_mem_threshold", DIAMOND_mem_default)
self.DETECT_mem_threshold = self.value_assignment(config, "Settings", "DETECT_mem_threshold", DETECT_mem_default)
self.Infernal_mem_threshold = self.value_assignment(config, "Settings", "Infernal_mem_threshold", Infernal_mem_default)
self.Barrnap_mem_threshold = self.value_assignment(config, "Settings", "Barrnap_mem_threshold", Barrnap_mem_default)
self.BWA_pp_mem_threshold = self.value_assignment(config, "Settings", "BWA_pp_mem_threshold", BWA_pp_mem_default)
self.BLAT_pp_mem_threshold = self.value_assignment(config, "Settings", "BLAT_pp_mem_threshold", BLAT_pp_mem_default)
self.DIAMOND_pp_mem_threshold = self.value_assignment(config, "Settings", "DIAMOND_pp_mem_threshold", DIAMOND_pp_mem_default)
self.GA_final_merge_mem_threshold = self.value_assignment(config, "Settings", "GA_final_merge_mem_threshold", GA_final_merge_mem_default)
self.TA_mem_threshold = self.value_assignment(config, "Settings", "TA_mem_threshold", TA_mem_threshold_default)
self.repop_mem_threshold = self.value_assignment(config, "Settings", "repop_mem_threshold", repop_mem_default)
self.EC_mem_threshold = self.value_assignment(config, "Settings", "EC_mem_threshold", EC_mem_threshold_default)
#-----------------------------------------------------------------------------------------------
self.BWA_job_limit = self.value_assignment(config, "Settings", "BWA_job_limit", BWA_job_limit_default)
self.BLAT_job_limit = self.value_assignment(config, "Settings", "BLAT_job_limit", BLAT_job_limit_default)
self.DIAMOND_job_limit = self.value_assignment(config, "Settings", "DIAMOND_job_limit", DIAMOND_job_limit_default)
self.DETECT_job_limit = self.value_assignment(config, "Settings", "DETECT_job_limit", DETECT_job_limit_default)
self.Infernal_job_limit = self.value_assignment(config, "Settings", "Infernal_job_limit", Infernal_job_limit_default)
self.Barrnap_job_limit = self.value_assignment(config, "Settings", "Barrnap_job_limit", Barrnap_job_limit_default)
self.BWA_pp_job_limit = self.value_assignment(config, "Settings", "BWA_pp_job_limit", BWA_pp_job_limit_default)
self.BLAT_pp_job_limit = self.value_assignment(config, "Settings", "BLAT_pp_job_limit", BLAT_pp_job_limit_default)
self.DIAMOND_pp_job_limit = self.value_assignment(config, "Settings", "DIAMOND_pp_job_limit", DIAMOND_pp_job_limit_default)
self.GA_final_merge_job_limit = self.value_assignment(config, "Settings", "GA_final_merge_job_limit", GA_final_merge_job_limit_default)
self.TA_job_limit = self.value_assignment(config, "Settings", "TA_job_limit", TA_job_limit_default)
self.repop_job_limit = self.value_assignment(config, "Settings", "repop_job_limit", repop_job_limit_default)
self.EC_job_limit = self.value_assignment(config, "Settings", "EC_job_limit", EC_job_limit_default)
self.Centrifuge_job_limit = self.value_assignment(config, "Settings", "Centrifuge_job_limit", Centrifuge_job_limit_default)
#------------------------------------------------------------------------
self.Infernal_job_delay = self.value_assignment(config, "Settings", "Infernal_job_delay", Infernal_job_delay_default)
self.Barrnap_job_delay = self.value_assignment(config, "Settings", "Barrnap_job_delay", Barrnap_job_delay_default)
self.BWA_job_delay = self.value_assignment(config, "Settings", "BWA_job_delay", BWA_job_delay_default)
self.BLAT_job_delay = self.value_assignment(config, "Settings", "BLAT_job_delay", BLAT_job_delay_default)
self.DIAMOND_job_delay = self.value_assignment(config, "Settings", "DIAMOND_job_delay", DIAMOND_job_delay_default)
self.DETECT_job_delay = self.value_assignment(config, "Settings", "DETECT_job_delay", DETECT_job_delay_default)
self.BWA_pp_job_delay = self.value_assignment(config, "Settings", "BWA_pp_job_delay", BWA_pp_job_delay_default)
self.BLAT_pp_job_delay = self.value_assignment(config, "Settings", "BLAT_pp_job_delay", BLAT_pp_job_delay_default)
self.DIAMOND_pp_job_delay = self.value_assignment(config, "Settings", "DIAMOND_pp_job_delay", DIAMOND_pp_job_delay_default)
self.GA_final_merge_job_delay = self.value_assignment(config, "Settings", "GA_final_merge_job_delay", GA_final_merge_job_delay_default)
self.TA_job_delay = self.value_assignment(config, "Settings", "TA_job_delay", TA_job_delay_default)
self.repop_job_delay = self.value_assignment(config, "Settings", "repop_job_delay", repop_job_delay_default)
self.EC_job_delay = self.value_assignment(config, "Settings", "EC_job_delay", EC_job_delay_default)
#------------------------------------------------------------------------------------------------
self.keep_all = self.value_assignment(config, "Settings", "keep_all", keep_all_default)
self.keep_quality = self.value_assignment(config, "Settings", "keep_quality", keep_quality_default)
self.keep_host = self.value_assignment(config, "Settings", "keep_host", keep_host_default)
self.keep_vector = self.value_assignment(config, "Settings", "keep_vector", keep_vector_default)
self.keep_rRNA = self.value_assignment(config, "Settings", "keep_rRNA", keep_rRNA_default)
self.keep_repop = self.value_assignment(config, "Settings", "keep_repop", keep_repop_default)
self.keep_assemble_contigs = self.value_assignment(config, "Settings", "keep_assemble_contigs", keep_assemble_contigs_default)
self.keep_GA_BWA = self.value_assignment(config, "Settings", "keep_GA_BWA", keep_GA_BWA_default)
self.keep_GA_BLAT = self.value_assignment(config, "Settings", "keep_GA_BLAT", keep_GA_BLAT_default)
self.keep_GA_DIAMOND = self.value_assignment(config, "Settings", "keep_GA_DIAMOND", keep_GA_DIAMOND_default)
self.keep_GA_final = self.value_assignment(config, "Settings", "keep_GA_final", keep_GA_final_default)
self.keep_TA = self.value_assignment(config, "Settings", "keep_TA", keep_TA_default)
self.keep_EC = self.value_assignment(config, "Settings", "keep_EC", keep_EC_default)
self.keep_outputs = self.value_assignment(config, "Settings", "keep_outputs", keep_outputs_default)
#--------------------------------------------------------------------------------------
self.filter_stringency = self.value_assignment(config, "Settings", "filter_stringency", filter_stringency_default)
self.GA_chunksize = self.value_assignment(config, "Settings", "GA_chunk_size", GA_chunksize_default)
self.EC_chunksize = self.value_assignment(config, "Settings", "EC_chunk_size", EC_chunksize_default)
self.rRNA_chunksize = self.value_assignment(config, "Settings", "rRNA_chunk_size", rRNA_chunksize_default)
#--------------------------------------------------------------------------------------------
# Labels.
# why? to change them during integration + new feature testing
quality_filter_label_default = "quality_filter"
host_filter_label_default = "host_filter"
vector_filter_label_default = "vector_filter"
rRNA_filter_label_default = "rRNA_filter"
rRNA_filter_split_label_default = "rRNA_filter_split"
rRNA_filter_convert_label_default = "rRNA_filter_convert"
rRNA_filter_barrnap_label_default = "rRNA_filter_barrnap"
rRNA_filter_barrnap_merge_label_default = "rRNA_filter_barrnap_merge"
rRNA_filter_barrnap_pp_label_default = "rRNA_filter_barrnap_pp"
rRNA_filter_infernal_label_default = "rRNA_filter_infernal"
rRNA_filter_infernal_prep_label_default = "rRNA_filter_infernal_prep"
rRNA_filter_splitter_label_default = "rRNA_filter_splitter"
rRNA_filter_post_label_default = "rRNA_filter_post"
repop_label_default = "duplicate_repopulation"
assemble_contigs_label_default = "assemble_contigs"
destroy_contigs_label_default = "destroy_contigs"
GA_pre_scan_label_default = "GA_pre_scan"
GA_split_label_default = "GA_split"
GA_BWA_label_default = "GA_BWA"
GA_BWA_pp_label_default = "GA_BWA_pp"
GA_BWA_merge_label_default = "GA_BWA_merge"
GA_BLAT_label_default = "GA_BLAT"
GA_BLAT_cleanup_label_default = "GA_BLAT_cleanup"
GA_BLAT_cat_label_default = "GA_BLAT_cat"
GA_BLAT_pp_label_default = "GA_BLAT_pp"
GA_BLAT_merge_label_default = "GA_BLAT_merge"
GA_DIAMOND_label_default = "GA_DMD"
GA_DIAMOND_pp_label_default = "GA_DMD_pp"
GA_final_merge_label_default = "GA_final_merge"
taxon_annotation_label_default = "taxonomic_annotation"
ec_annotation_label_default = "enzyme_annotation"
ec_annotation_detect_label_default = "enzyme_annotation_detect"
ec_annotation_priam_label_default = "enzyme_annotation_priam"
ec_annotation_priam_split_label_default = "enzyme_annotation_priam_split"
ec_annotation_priam_cat_label_default = "enzyme_annotation_priam_cat"
ec_annotation_DIAMOND_label_default = "enzyme_annotation_DMD"
ec_annotation_pp_label_default = "enzyme_annotation_pp"
output_label_default = "outputs"
output_copy_gene_map_label_default = "output_copy_gene_map"
output_clean_EC_label_default = "output_clean_ec"
output_copy_taxa_label_default = "output_copy_taxa"
output_network_gen_label_default = "output_network_generation"
output_unique_hosts_singletons_label_default = "output_unique_hosts_singletons"
output_unique_hosts_pair_1_label_default = "output_unique_hosts_pair_1"
output_unique_hosts_pair_2_label_default = "output_unique_hosts_pair_2"
output_unique_vectors_singletons_label_default = "output_unique_vectors_singletons"
output_unique_vectors_pair_1_label_default = "output_unique_vectors_pair_1"
output_unique_vectors_pair_2_label_default = "output_unique_vectors_pair_2"
output_combine_hosts_label_default = "output_combine_hosts"
output_per_read_scores_label_default = "output_per_read_scores"
output_contig_stats_label_default = "output_contig_stats"
output_ec_heatmap_label_default = "output_ec_heatmap"
output_taxa_groupby_label_default = "output_taxa_groupby"
output_read_count_label_default = "output_read_count"
self.quality_filter_label = self.value_assignment(config, "Labels", "quality_filter", quality_filter_label_default)
self.host_filter_label = self.value_assignment(config, "Labels", "host_filter", host_filter_label_default)
self.vector_filter_label = self.value_assignment(config, "Labels", "vector_filter", vector_filter_label_default)
self.rRNA_filter_label = self.value_assignment(config, "Labels", "rRNA_filter", rRNA_filter_label_default)
self.rRNA_filter_split_label = self.value_assignment(config, "Labels", "rRNA_filter_split", rRNA_filter_split_label_default)
self.rRNA_filter_convert_label = self.value_assignment(config, "Labels", "rRNA_filter_convert", rRNA_filter_convert_label_default)
self.rRNA_filter_barrnap_label = self.value_assignment(config, "Labels", "rRNA_filter_barrnap", rRNA_filter_barrnap_label_default)
self.rRNA_filter_barrnap_merge_label = self.value_assignment(config, "Labels", "rRNA_filter_barrnap_merge", rRNA_filter_barrnap_merge_label_default)
self.rRNA_filter_barrnap_pp_label = self.value_assignment(config, "Labels", "rRNA_filter_barrnap_pp", rRNA_filter_barrnap_pp_label_default)
self.rRNA_filter_infernal_label = self.value_assignment(config, "Labels", "rRNA_filter_infernal", rRNA_filter_infernal_label_default)
self.rRNA_filter_infernal_prep_label = self.value_assignment(config, "Labels", "rRNA_filter_infernal_prep", rRNA_filter_infernal_prep_label_default)
self.rRNA_filter_splitter_label = self.value_assignment(config, "Labels", "rRNA_filter_splitter", rRNA_filter_splitter_label_default)
self.rRNA_filter_post_label = self.value_assignment(config, "Labels", "rRNA_filter_post", rRNA_filter_post_label_default)
self.repop_label = self.value_assignment(config, "Labels", "repop", repop_label_default)
self.assemble_contigs_label = self.value_assignment(config, "Labels", "assemble_contigs", assemble_contigs_label_default)
self.destroy_contigs_label = self.value_assignment(config, "Labels", "destroy_contigs", destroy_contigs_label_default)
self.GA_pre_scan_label = self.value_assignment(config, "Labels", "GA_pre_scan", GA_pre_scan_label_default)
self.GA_split_label = self.value_assignment(config, "Labels", "GA_split", GA_split_label_default)
self.GA_BWA_label = self.value_assignment(config, "Labels", "GA_BWA", GA_BWA_label_default)
self.GA_BWA_pp_label = self.value_assignment(config, "Labels", "GA_BWA_pp", GA_BWA_pp_label_default)
self.GA_BWA_merge_label = self.value_assignment(config, "Labels", "GA_BWA_merge", GA_BWA_merge_label_default)
self.GA_BLAT_label = self.value_assignment(config, "Labels", "GA_BLAT", GA_BLAT_label_default)
self.GA_BLAT_cleanup_label = self.value_assignment(config, "Labels", "GA_BLAT_cleanup", GA_BLAT_cleanup_label_default)
self.GA_BLAT_cat_label = self.value_assignment(config, "Labels", "GA_BLAT_cat", GA_BLAT_cat_label_default)
self.GA_BLAT_pp_label = self.value_assignment(config, "Labels", "GA_BLAT_pp", GA_BLAT_pp_label_default)
self.GA_BLAT_merge_label = self.value_assignment(config, "Labels", "GA_BLAT_merge", GA_BLAT_merge_label_default)
self.GA_DIAMOND_label = self.value_assignment(config, "Labels", "GA_DIAMOND", GA_DIAMOND_label_default)
self.GA_DIAMOND_pp_label = self.value_assignment(config, "Labels", "GA_DIAMOND_pp", GA_DIAMOND_pp_label_default)
self.GA_final_merge_label = self.value_assignment(config, "Labels", "GA_final_merge", GA_final_merge_label_default)
self.ta_label = self.value_assignment(config, "Labels", "ta", taxon_annotation_label_default)
self.ec_label = self.value_assignment(config, "Labels", "ec", ec_annotation_label_default)
self.ec_detect_label = self.value_assignment(config, "Labels", "ec_detect", ec_annotation_detect_label_default)
self.ec_priam_label = self.value_assignment(config, "Labels", "ec_priam", ec_annotation_priam_label_default)
self.ec_priam_split_label = self.value_assignment(config, "Labels", "ec_priam_split", ec_annotation_priam_split_label_default)
self.ec_priam_cat_label = self.value_assignment(config, "Labels", "ec_priam_cat", ec_annotation_priam_cat_label_default)
self.ec_DIAMOND_label = self.value_assignment(config, "Labels", "ec_DIAMOND", ec_annotation_DIAMOND_label_default)
self.ec_pp_label = self.value_assignment(config, "Labels", "ec_pp", ec_annotation_pp_label_default)
self.output_label = self.value_assignment(config, "Labels", "outputs", output_label_default)
self.output_copy_gene_map_label = self.value_assignment(config, "Labels", "output_copy_gene_map", output_copy_gene_map_label_default)
self.output_clean_ec_label = self.value_assignment(config, "Labels", "output_clean_ec", output_clean_EC_label_default)
self.output_copy_taxa_label = self.value_assignment(config, "Labels", "output_copy_taxa", output_copy_taxa_label_default)
self.output_network_generation_label = self.value_assignment(config, "Labels", "output_network_generation", output_network_gen_label_default)
self.output_unique_hosts_singletons_label = self.value_assignment(config, "Labels", "output_unique_hosts_singletons", output_unique_hosts_singletons_label_default)
self.output_unique_hosts_pair_1_label = self.value_assignment(config, "Labels", "output_unique_hosts_pair_1", output_unique_hosts_pair_1_label_default)
self.output_unique_hosts_pair_2_label = self.value_assignment(config, "Labels", "output_unique_hosts_pair_2", output_unique_hosts_pair_2_label_default)
self.output_unique_vectors_singletons_label = self.value_assignment(config, "Labels", "output_unique_vectors_singletons", output_unique_vectors_singletons_label_default)
self.output_unique_vectors_pair_1_label = self.value_assignment(config, "Labels", "output_unique_vectors_pair_1", output_unique_vectors_pair_1_label_default)
self.output_unique_vectors_pair_2_label = self.value_assignment(config, "Labels", "output_unique_vectors_pair_2", output_unique_vectors_pair_2_label_default)
self.output_combine_hosts_label = self.value_assignment(config, "Labels", "output_combine_hosts", output_combine_hosts_label_default)
self.output_per_read_scores_label = self.value_assignment(config, "Labels", "output_per_read_scores", output_per_read_scores_label_default)
self.output_contig_stats_label = self.value_assignment(config, "Labels", "output_contig_stats", output_contig_stats_label_default)
self.output_ec_heatmap_label = self.value_assignment(config, "Labels", "output_ec_heatmap", output_ec_heatmap_label_default)
self.output_taxa_groupby_label = self.value_assignment(config, "Labels", "output_taxa_groupby", output_taxa_groupby_label_default)
self.output_read_count_label = self.value_assignment(config, "Labels", "output_read_count", output_read_count_label_default)
#----------------------------------------------------------
# Reference Databases
# Note: default host is Mouse CDS
#if config:
self.UniVec_Core = self.value_assignment(config, "Databases", "UniVec_Core", os.path.join(database_path, "univec_core/UniVec_Core.fasta"))
self.Adapter = self.value_assignment(config, "Databases", "Adapter", os.path.join(database_path, "Trimmomatic_adapters/TruSeq3-PE-2.fa"))
self.Host = self.value_assignment(config, "Databases", "Host", os.path.join(database_path, "Mouse_cds/Mouse_cds.fasta"))
self.Rfam = self.value_assignment(config, "Databases", "Rfam", os.path.join(database_path, "Rfam/Rfam.cm"))
self.DNA_DB = self.value_assignment(config, "Databases", "DNA_DB", os.path.join(database_path, "ChocoPhlAn/ChocoPhlAn.fasta"))
self.source_taxa_DB = self.value_assignment(config, "Databases", "source_taxa_db", os.path.join(database_path, "family_llbs"))
self.Prot_DB = self.value_assignment(config, "Databases", "Prot_DB", os.path.join(database_path, "nr/nr"))
self.Prot_DB_reads = self.value_assignment(config, "Databases", "Prot_DB_reads", os.path.join(database_path, "nr/nr"))
self.accession2taxid = self.value_assignment(config, "Databases", "accession2taxid", os.path.join(database_path, "accession2taxid/accession2taxid"))
self.nodes = self.value_assignment(config, "Databases", "nodes", os.path.join(database_path, "WEVOTE_db", "nodes.dmp"))
self.names = self.value_assignment(config, "Databases", "names", os.path.join(database_path, "WEVOTE_db", "names.dmp"))
self.Kaiju_db = self.value_assignment(config, "Databases", "Kaiju_db", os.path.join(database_path, "kaiju_db/kaiju_db_nr.fmi"))
self.Centrifuge_db = self.value_assignment(config, "Databases", "Centrifuge_db", os.path.join(database_path, "centrifuge_db/nt"))
self.SWISS_PROT = self.value_assignment(config, "Databases", "SWISS_PROT", os.path.join(database_path, "swiss_prot_db/swiss_prot_db"))
self.SWISS_PROT_map = self.value_assignment(config, "Databases", "SWISS_PROT_map", os.path.join(database_path, "swiss_prot_db/SwissProt_EC_Mapping.tsv"))
self.PriamDB = self.value_assignment(config, "Databases", "PriamDB", os.path.join(database_path, "PRIAM_db/"))
self.DetectDB = self.value_assignment(config, "Databases", "DetectDB", os.path.join(database_path, "DETECTv2"))
self.WEVOTEDB = self.value_assignment(config, "Databases", "WEVOTEDB", os.path.join(database_path, "WEVOTE_db/"))
self.EC_pathway = self.value_assignment(config, "Databases", "EC_pathway", os.path.join(database_path, "EC_pathway.txt"))
self.path_to_superpath = self.value_assignment(config, "Databases", "path_to_superpath", os.path.join(custom_database_path, "pathway_to_superpathway.csv"))
self.mgm_model = self.value_assignment(config, "Databases", "MetaGeneMark_model", os.path.join(tool_path, "mgm/MetaGeneMark_v1.mod"))
self.enzyme_db = self.value_assignment(config, "Databases", "enzyme_db", os.path.join(custom_database_path, "FREQ_EC_pairs_3_mai_2020.txt"))
self.taxid_tree = self.value_assignment(config, "Databases", "taxid_tree", os.path.join(custom_database_path, "taxid_trees", "family_tree.tsv"))
self.kraken2_db = self.value_assignment(config, "Databases", "kraken2_db", os.path.join(custom_database_path, "kraken2_db"))
#-------------------------------------------------------
# test DBs
self.GA_DB_mode = "multi" #by default for the new DB changes.
self.check_dmd_valid()
if(self.DNA_DB_mode == "custom"):
self.check_bwa_valid(self.DNA_DB)
self.check_blat_valid(self.DNA_DB)
#----------------------------------------------------------
# external tools
#if config:
self.Python = self.value_assignment(config, "Tools", "Python", "python3")
self.Java = self.value_assignment(config, "Tools", "Java", "java -jar")
self.cdhit_dup = self.value_assignment(config, "Tools", "cdhit_dup", os.path.join(tool_path, "cdhit_dup/cd-hit-dup"))
self.AdapterRemoval = self.value_assignment(config, "Tools", "AdapterRemoval", os.path.join(tool_path, "adapterremoval/AdapterRemoval"))
self.vsearch = self.value_assignment(config, "Tools", "vsearch", os.path.join(tool_path, "vsearch/vsearch"))
self.BWA = self.value_assignment(config, "Tools", "BWA", os.path.join(tool_path, "BWA/bwa"))
self.SAMTOOLS = self.value_assignment(config, "Tools", "SAMTOOLS", os.path.join(tool_path, "samtools/samtools"))
self.BLAT = self.value_assignment(config, "Tools", "BLAT", os.path.join(tool_path, "PBLAT/pblat"))
self.DIAMOND = self.value_assignment(config, "Tools", "DIAMOND", os.path.join(tool_path, "DIAMOND/diamond"))
self.Blastp = self.value_assignment(config, "Tools", "Blastp", os.path.join(tool_path, "BLAST_p/blastp"))
self.Needle = self.value_assignment(config, "Tools", "Needle", os.path.join(tool_path, "EMBOSS-6.6.0/emboss/stretcher"))
self.Makeblastdb = self.value_assignment(config, "Tools", "Makeblastdb", os.path.join(tool_path, "BLAST_p/makeblastdb"))
self.Barrnap = self.value_assignment(config, "Tools", "Barrnap", os.path.join(tool_path, "Barrnap/bin/barrnap"))
self.Infernal = self.value_assignment(config, "Tools", "Infernal", os.path.join(tool_path, "infernal/cmsearch"))
self.Kaiju = self.value_assignment(config, "Tools", "Kaiju", os.path.join(tool_path, "kaiju/kaiju"))
self.Centrifuge = self.value_assignment(config, "Tools", "Centrifuge", os.path.join(tool_path, "centrifuge/centrifuge"))
self.Priam = self.value_assignment(config, "Tools", "Priam", os.path.join(tool_path, "PRIAM_search/PRIAM_search.jar"))
self.Detect = self.value_assignment(config, "Tools", "Detect", os.path.join(script_path, "Detect_2.2.10.py"))
self.BLAST_dir = self.value_assignment(config, "Tools", "BLAST_dir", os.path.join(tool_path, "BLAST_p"))
self.WEVOTE = self.value_assignment(config, "Tools", "WEVOTE", os.path.join(tool_path, "WEVOTE/WEVOTE"))
self.Spades = self.value_assignment(config, "Tools", "Spades", os.path.join(tool_path, "SPAdes/bin/spades.py"))
self.MetaGeneMark = self.value_assignment(config, "Tools", "MetaGeneMark", os.path.join(tool_path, "mgm/gmhmmp"))
self.kraken2 = self.value_assignment(config, "Tools", "kraken2", os.path.join(tool_path, "kraken2/kraken2"))
#--------------------------------------------
# Python scripts
#if config:
self.sam_trimmer = self.value_assignment(config, "code", "sam_trimmer", os.path.join(script_path, "read_sam.py"))
self.sort_reads = self.value_assignment(config, "code", "sort_reads", os.path.join(script_path, "read_sort.py"))
self.duplicate_repopulate = self.value_assignment(config, "code", "duplicate_repopulation", os.path.join(script_path, "read_repopulation.py"))
self.orphaned_read_filter = self.value_assignment(config, "code", "orphaned_read_filter", os.path.join(script_path, "read_orphan.py"))
self.remove_tag = self.value_assignment(config, "code", "remove_tag", os.path.join(script_path, "read_remove_tag.py"))
self.BLAT_Contaminant_Filter = self.value_assignment(config, "code", "blat_contaminant_filter", os.path.join(script_path, "read_BLAT_filter_v3.py"))
self.File_splitter = self.value_assignment(config, "code", "file_splitter", os.path.join(script_path, "read_split.py"))
self.barrnap_post = self.value_assignment(config, "code", "barrnap_post", os.path.join(script_path, "read_rRNA_barrnap.py"))
self.rRNA_filter = self.value_assignment(config, "code", "rRNA_filter", os.path.join(script_path, "read_rRNA_infernal.py"))
self.Map_contig = self.value_assignment(config, "code", "map_contig", os.path.join(script_path, "assembly_make_contig_map.py"))
self.flush_bad_contigs = self.value_assignment(config, "code", "flush_bad_contigs", os.path.join(script_path, "assembly_flush_bad_contigs.py"))
self.contig_duplicate_remover = self.value_assignment(config, "code", "contig_duplicate_remover", os.path.join(script_path, "assembly_deduplicate.py"))
self.Map_reads_gene_BWA = self.value_assignment(config, "code", "ga_bwa_pp", os.path.join(script_path, "ga_BWA_generic_v2.py"))
self.Map_reads_gene_BLAT = self.value_assignment(config, "code", "ga_blat_pp", os.path.join(script_path, "ga_BLAT_generic_v3.py"))
self.Map_reads_prot_DMND = self.value_assignment(config, "code", "ga_dmd_pp", os.path.join(script_path, "ga_Diamond_generic_v2.py"))
self.GA_final_merge = self.value_assignment(config, "code", "ga_final_merge", os.path.join(script_path, "ga_Final_merge_v4.py"))
self.GA_merge_fasta = self.value_assignment(config, "code", "ga_merge_fasta", os.path.join(script_path, "ga_merge_fasta.py"))
self.GA_final_merge_fasta = self.value_assignment(config, "code", "ga_final_merge_fasta", os.path.join(script_path, "ga_final_merge_fastq.py"))
self.GA_final_merge_proteins = self.value_assignment(config, "code", "ga_final_merge_proteins", os.path.join(script_path, "ga_final_merge_proteins.py"))
self.GA_final_merge_maps = self.value_assignment(config, "code", "ga_final_merge_maps", os.path.join(script_path, "ga_final_merge_map.py"))
self.EC_Annotation_Post = self.value_assignment(config, "code", "ec_combine", os.path.join(script_path, "ea_combine_v5.py"))
self.Annotated_taxid = self.value_assignment(config, "code", "ta_taxid", os.path.join(script_path, "ta_taxid_v3.py"))
self.Constrain_classification = self.value_assignment(config, "code", "ta_constrain", os.path.join(script_path, "ta_constrain_taxonomy_v2.py"))
self.Classification_combine = self.value_assignment(config, "code", "ta_combine", os.path.join(script_path, "ta_combine_v3.py"))
self.Wevote_parser = self.value_assignment(config, "code", "ta_wevote", os.path.join(script_path, "ta_wevote_parser.py"))
self.taxa_table = self.value_assignment(config, "code", "output_taxa", os.path.join(script_path, "output_taxa_groupby.py"))
self.RPKM = self.value_assignment(config, "code", "output_rpkm", os.path.join(script_path, "output_table_v3.py"))
self.format_RPKM = self.value_assignment(config, "code", "output_reformat", os.path.join(script_path, "output_reformat_rpkm_table.py"))
self.read_count = self.value_assignment(config, "code", "output_read_count", os.path.join(script_path, "output_read_counts_v2.py"))
self.read_quality_metrics = self.value_assignment(config, "code", "output_qual", os.path.join(script_path, "output_read_quality_metrics.py"))
self.contig_stats = self.value_assignment(config, "code", "output_contig_stats", os.path.join(script_path, "output_contig_stats.py"))
self.ec_heatmap = self.value_assignment(config, "code", "output_heatmap", os.path.join(script_path, "output_EC_metrics.py"))
self.data_change_metrics = self.value_assignment(config, "code", "output_data_change", os.path.join(script_path, "output_data_change_metrics.py"))
self.get_unique_host_reads = self.value_assignment(config, "code", "output_unique_hosts", os.path.join(script_path, "output_get_host_reads.py"))
self.remove_gaps_in_fasta = self.value_assignment(config, "code", "remove_fasta_gaps", os.path.join(script_path, "remove_gaps_in_fasta.py"))
self.parse_sam = self.value_assignment(config, "code", "output_sam", os.path.join(script_path, "output_parse_sam.py"))
self.are_you_in_a_contig = self.value_assignment(config, "code", "output_contig_check", os.path.join(script_path, "output_are_you_in_a_contig.py"))
self.convert_contig_segments = self.value_assignment(config, "code", "output_convert_gene_map", os.path.join(script_path, "output_convert_gene_map_contig_segments.py"))
self.output_filter_taxa = self.value_assignment(config, "code", "output_filter_taxa", os.path.join(script_path, "output_filter_taxa.py"))
self.output_filter_ECs = self.value_assignment(config, "code", "output_filter_ec", os.path.join(script_path, "output_filter_ECs.py"))
self.bwa_read_sorter = self.value_assignment(config, "code", "bwa_read_sorter", os.path.join(script_path, "bwa_read_sorter.py"))
self.ta_contig_name_convert = self.value_assignment(config, "code", "ta_name_convert", os.path.join(script_path, "ta_contig_name_convert.py"))
self.GA_pre_scan_get_lib = self.value_assignment(config, "code", "ga_pre_scan_get_lib", os.path.join(script_path, "ga_pre_scan_get_libs.py"))
self.GA_pre_scan_assemble_lib = self.value_assignment(config, "code", "ga_pre_scan_assemble_lib", os.path.join(script_path, "ga_pre_scan_assemble_libs.py"))