def customize_catfam(architect_location, parameter_values, project_name,
output_dir, i_to_num_split):
current_folder = output_dir + "/" + project_name + "/CatFam"
mkdir_if_not_exists(current_folder)
num_to_new_line = {}
num_to_new_line[4] = "#SBATCH --job-name=CatFam_" + project_name
num_to_new_line[7] = "PATH=$PATH:" + parameter_values["BLAST_DIR"]
num_to_new_line[10] = "cd " + current_folder
num_to_new_line[13] = "CATFAM_DIR=" + parameter_values["CATFAM_DIR"]
utils.copy_and_replace(architect_location + "/scripts/individual_enzyme_annotation/CatFam/run_catfam.sh", \
current_folder + "/run_catfam.sh", num_to_new_line)
mkdir_if_not_exists(current_folder + "/Split_seqs", True)
write_split_seqs(current_folder + "/Split_seqs", i_to_num_split,
parameter_values["SEQUENCE_FILE"])
def customize_detect(architect_location, parameter_values, project_name,
output_dir, time):
current_folder = output_dir + "/" + project_name + "/DETECT"
mkdir_if_not_exists(current_folder)
num_to_new_line = {}
num_to_new_line[3] = "#SBATCH --time=" + str(time) + ":00:00"
num_to_new_line[4] = "#SBATCH --job-name=DETECT_" + project_name
num_to_new_line[
7] = "DETECT_TOOL=" + parameter_values["DETECT_DIR"] + "/detect.py"
num_to_new_line[
10] = "export PATH=" + parameter_values["DETECT_DIR"] + "/:$PATH"
num_to_new_line[
11] = "export PATH=" + parameter_values["EMBOSS_DIR"] + "/:$PATH"
num_to_new_line[22] = "cd " + current_folder
num_to_new_line[28] = "SEQ_NAME=" + parameter_values["SEQUENCE_FILE"]
utils.copy_and_replace(architect_location + "/scripts/individual_enzyme_annotation/DETECT/run_detect.sh", \
current_folder + "/run_detect.sh", num_to_new_line)
def customize_priam(architect_location, parameter_values, project_name,
output_dir, time):
current_folder = output_dir + "/" + project_name + "/PRIAM"
mkdir_if_not_exists(current_folder)
num_to_new_line = {}
num_to_new_line[3] = "#SBATCH --time=" + str(time) + ":00:00"
num_to_new_line[4] = "#SBATCH --job-name=PRIAM_" + project_name
num_to_new_line[7] = "my_WORKDIR=" + current_folder
num_to_new_line[8] = "TEST=" + parameter_values["SEQUENCE_FILE"]
num_to_new_line[9] = "PRIAM_SEARCH=" + parameter_values["PRIAM_DIR"]
num_to_new_line[
10] = "PRIAM_profiles_library=" + parameter_values["PRIAM_db"]
num_to_new_line[22] = "BLAST_BIN=" + parameter_values["BLAST_DIR"]
utils.copy_and_replace(
architect_location +
"/scripts/individual_enzyme_annotation/PRIAM/run_priam.sh",
current_folder + "/run_priam.sh", num_to_new_line)
def customize_enzdp(architect_location, parameter_values, project_name,
output_dir, i_to_num_split):
current_folder = output_dir + "/" + project_name + "/EnzDP"
mkdir_if_not_exists(current_folder)
utils.copy_and_replace(
architect_location +
"/scripts/individual_enzyme_annotation/EnzDP/individualize_project.sh",
current_folder + "/individualize_project.sh", {})
num_to_new_line = {}
num_to_new_line[
3] = "FASTA_FILE='" + current_folder + "/Split_seqs/SEQ_NAME'"
num_to_new_line[
5] = "OUTPUT_FILE='" + current_folder + "/Results/SEQ_NAME.out'"
utils.copy_and_replace(
architect_location +
"/scripts/individual_enzyme_annotation/EnzDP/TEMPLATE_project.py",
current_folder + "/TEMPLATE_project.py", num_to_new_line)
num_to_new_line = {}
num_to_new_line[4] = "#SBATCH --job-name=EnzDP_" + project_name
num_to_new_line[7] = "ENZDP_TOOL=" + parameter_values["EnzDP_DIR"]
num_to_new_line[11] = "folder=" + current_folder
utils.copy_and_replace(
architect_location +
"/scripts/individual_enzyme_annotation/EnzDP/run_enzdp.sh",
current_folder + "/run_enzdp.sh", num_to_new_line)
mkdir_if_not_exists(current_folder + "/Split_seqs", True)
write_split_seqs(current_folder + "/Split_seqs", i_to_num_split,
parameter_values["SEQUENCE_FILE"])
def customize_eficaz(architect_location, parameter_values, project_name,
output_dir, i_to_num_split):
current_folder = output_dir + "/" + project_name + "/EFICAz"
mkdir_if_not_exists(current_folder)
utils.copy_and_replace(
architect_location +
"/scripts/individual_enzyme_annotation/EFICAz/individualize.sh",
current_folder + "/individualize.sh", {})
num_to_new_line = {}
num_to_new_line[
4] = "#SBATCH --job-name=EFICAz_" + project_name + "_SEQUENCE_FILENAME_X1"
num_to_new_line[7] = "EFICAz25_PATH=" + parameter_values["EFICAz_DIR"]
num_to_new_line[14] = "cd " + current_folder
num_to_new_line[105] = "\tmy_scratch=" + current_folder + "/Results"
utils.copy_and_replace(architect_location + "/scripts/individual_enzyme_annotation/EFICAz/TEMPLATE_eficaz.sh", \
current_folder + "/TEMPLATE_eficaz.sh", num_to_new_line)
mkdir_if_not_exists(current_folder + "/Split_seqs", True)
write_split_seqs(current_folder + "/Split_seqs", i_to_num_split,
parameter_values["SEQUENCE_FILE"])
"--ec_preds_file ${ENZ_ANNOTATION_results} --database ${DATABASE} --output_folder ${OUTPUT_FOLDER} " +\
"--penalty_exchange " + str(penalty_deadend)
line_to_new_text[44] = new_create_scores_command
perform_gap_fill_command = "python3.7 " + gapfill_script + " " + \
temp_folder + "/SIMULATION_high_confidence_reactions_plus_essentials.xml -m M9 -o " + \
temp_folder + "/model_gapfilled_multi_" + str(num_solns) + ".lst --scoredb " + \
temp_folder + "/SIMULATION_reaction_scores.out " + \
"--universe-file " + temp_folder + "/SIMULATED_reduced_universe_with_fva.xml " + \
"--pool-size ${NUM_SOLNS} --pool-gap " + str(pool_gap)
if integrality_tolerance != "":
perform_gap_fill_command = perform_gap_fill_command + " --integrality-tolerance " + str(
integrality_tolerance)
line_to_new_text[49] = perform_gap_fill_command
template_file = architect_path + "/scripts/model_reconstruction/TEMPLATE_run_reconstruction.sh"
file_to_run = main_folder_with_recon_results + "/make_reconstruction.sh"
utils.copy_and_replace(template_file, file_to_run, line_to_new_text)
subprocess.call(["sh", file_to_run])
status_writer.write("Step 5: " + str(datetime.datetime.now()) +
": Gap-filling done.\n")
status_writer.close()
if not within_docker:
utils.print_with_colours(
"Architect: Thank you for using our tool today! Reconstruction is now done. Find your results under: "
+ final_output_folder)
else:
utils.print_with_colours(
"Architect: Thank you for using our tool today! Reconstruction is now done."
)