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Configmaker_samples_3.py
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Configmaker_samples_3.py
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#!/usr/bin/python
### When chosen assembly is "per sample"
project = str(input("Name of your project (leave blank to use default): "))
if project == "":
project_line = "\"project\" : " +"\"" + "My_project" +"\","
else:
project_line = "\"project\" : " +"\"" + project +"\","
host_removal = str(input("Do you want to remove host DNA from the analysis? (yes/no): "))
if host_removal == "yes":
host_removal_line = "\"host_removal\" : " + "True" + ","
elif host_removal == "no":
host_removal_line = "\"host_removal\" : " + "False" + ","
else:
print("Error: unvalid option, please type'yes' or 'no'")
reference = str(input("Do you have your own reference genome? (yes/no): "))
if reference == "no":
reference_line = "\"reference\" : " +"\"" + "data/test-data/reference/beta-vulgaris-subset.fasta" +"\","
reference_index_line = "\"reference_index\" : " +"\"" + "/data/shared/genomes/Eukaryotes/Phaseolus_vulgaris/GCA_000499845.1_PhaVulg1_0_genomic" +"\","
elif reference == "yes":
own_ref = str(input("Path to your reference genome: "))
own_ref_index = str(input("Path to the index file of your reference genome: "))
reference_line = "\"reference\" : " +"\"" + own_ref +"\","
reference_index_line = "\"reference_index\" : " +"\"" + own_ref_index +"\","
assembler = str(input("Choose an assembler (megahit/spades) (Default is megahit): "))
if assembler == "megahit" or assembler == "":
assembler_line = "\"assembler\" : " +"\"" + "megahit" +"\","
elif assembler == "spades":
assembler_line = "\"assembler\" : " +"\"" + assembler +"\","
else:
print("Error: please type a valid option")
x_0 = "{{{0} " ## Open dict
x_1 = "}}{0}" ## Close dict
tmpdir_line = "\"tmpdir\" : " +"\"" + "/tmp" +"\","
adapters_line = "\"adapters\" : " +"\"" + "/data/shared/tools/Trimmomatic/0.36/adapters/NexteraPE-PE.fa" +"\","
min_qual_line = "\"min_qual\" : " +"\"" + "30" +"\","
min_length_line = "\"min_length\" : " +"\"" + "150" +"\","
emapper_database_line = "\"emapper_database\" : " +"\"" + "/data/shared/db/eggnogdb/5.0.0" +"\","
emapper_diamond_line = "\"emapper_diamond\" : " +"\"" + "/data/shared/db/eggnogdb/5.0.0/eggnog_proteins.dmnd" +"\","
CAT_database_line = "\"CAT_database\" : " +"\"" + "/data/shared/db/CAT/CAT_prepare_20200618/2020-06-18_CAT_database/" +"\","
CAT_taxonomy_line = "\"CAT_taxonomy\" : " +"\"" + "/data/shared/db/CAT/CAT_prepare_20200618/2020-06-18_taxonomy/" +"\","
filter_contigs_length_line = "\"filter_contigs_length\" : " +"\"" + "2000" +"\","
filter_contigs_antismash_line = "\"filter_contigs_antismash\" : " +"\"" + "5000" +"\","
binner_line = '\"binner\" : ' + '["metabat", "vamb"]' + ','
big_line = "\"big\" : " +"\"" + "bigscape" +"\","
kmers_line = "\"kmers\" : " +"\"" + "33,55,77,99,127" +"\","
assembly_klist_line = "\"assembly-klist\" : "
meta_large_line = "\"meta-large\" : " +"\"" + "27,37,47,57,67,77,87,97,107,117,127" +"\","
data_line = "\"data\" : "
treatment_line = "\"treatment\" : "
import os
data_path = str(input("Where are your input files? (Please follow the format /path/) (Leave blank to use default): "))
if data_path == "":
data_path_line = 'data/'
else:
data_path_line = data_path
files = os.listdir(data_path_line)
for i in files:
if i.startswith(".")== True:
files.remove(i)
files.sort()
forward_list = list()
reverse_list = list()
for i in files:
if "_R1_" in i:
forward_list.append(i)
elif "_R2_" in i:
reverse_list.append(i)
lista_para_nombresdelinea = files
main_name_list = list()
for i in lista_para_nombresdelinea:
split_string = i.split(".")
main_name = split_string[0]
main_name_2 = main_name.split("_R")
if len(main_name_2) == 2:
main_name_list.append(main_name_2[0])
else:
print("An unvalid name has been found between your files. Please rename and execute again")
main_name_list = list(dict.fromkeys(main_name_list))
main_dict ={}
small_dict = {}
with open("config.json", "w") as file:
file.write('{\n')
file.write(' ' + project_line + '\n')
file.write(' ' + tmpdir_line + '\n')
file.write(' ' + adapters_line + '\n')
file.write(' ' + min_qual_line + '\n')
file.write(' ' + min_length_line + '\n')
file.write(' ' + host_removal_line + '\n')
file.write(' ' + reference_line + '\n')
file.write(' ' + reference_index_line + '\n')
file.write(' ' + emapper_database_line + '\n')
file.write(' ' + emapper_diamond_line + '\n')
file.write(' ' + CAT_database_line + '\n')
file.write(' ' + CAT_taxonomy_line + '\n')
file.write(' ' + filter_contigs_length_line + '\n')
file.write(' ' + filter_contigs_antismash_line + '\n')
file.write(' ' + assembler_line + '\n')
file.write(' ' + binner_line + '\n')
file.write(' ' + big_line + '\n')
file.write(' ' + kmers_line + '\n')
file.write(' ' + assembly_klist_line + x_0.format("") + '\n')
file.write(' ' + ' ' + meta_large_line + '\n')
file.write(' ' + x_1.format("") + "," '\n')
file.write(' ' + treatment_line + x_0.format("") + '\n')
for i in range(len(main_name_list)):
if i == len(main_name_list)-1:
file.write(' ' + ' ' + "\"" + main_name_list[i] + '" : ["' + main_name_list[i] + '"]' + '\n')
else:
file.write(' ' + ' ' + "\"" + main_name_list[i] + '" : ["' + main_name_list[i] + '"],' + '\n')
file.write(' ' + x_1.format("") + "," + '\n')
file.write(' ' + data_line + x_0.format("") + '\n')
## This is for printing the data (samples)
for i in range(len(main_name_list)):
with open("config.json", "a") as file:
if i == len(main_name_list)-1:
file.write(' ' + ' ' + "\"" + main_name_list[i] + '": {"forward": ' + "\"" + data_path_line + forward_list[i] + "\"" + ', "rev": ' + "\"" + data_path_line + reverse_list[i] + "\"}" + '\n')
else:
file.write(' ' + ' ' + "\"" + main_name_list[i] + '": {"forward": ' + "\"" + data_path_line + forward_list[i] + "\"" + ', "rev": ' + "\"" + data_path_line + reverse_list[i] + "\"}," + '\n')
with open("config.json", "a") as file:
file.write(' ' + x_1.format("") + '\n')
file.write(x_1.format("") + '\n')
print("Configuration file successfully created. Chosen assembly mode: individual assemblies")