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v1.7.3.3
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@Kinggerm
Kinggerm committed Feb 10, 2021
1 parent 711e275 commit 9354399
Showing 1 changed file with 49 additions and 25 deletions.
74 changes: 49 additions & 25 deletions Utilities/get_organelle_config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -130,13 +130,15 @@ def get_options(description):
with open(version_file) as open_version:
for line in open_version:
db_type, db_version, db_hash = line.strip().split("\t")
db_version = find_version(db_type, db_hash, SEED_DB_HASH, db_version)
sys.stdout.write(db_type + " Seed Database:\t" + db_version + "\t" + db_hash + "\n")
if options.db_type in ("label", "both"):
version_file = os.path.join(_LBL_DB_PATH, "VERSION")
if os.path.isfile(version_file):
with open(version_file) as open_version:
for line in open_version:
db_type, db_version, db_hash = line.strip().split("\t")
db_version = find_version(db_type, db_hash, LABEL_DB_HASH, db_version)
sys.stdout.write(db_type + " Label Database:\t" + db_version + "\t" + db_hash + "\n")
sys.exit()

Expand Down Expand Up @@ -204,7 +206,7 @@ def get_options(description):
sys.stdout.write("File " + this_fas_f + " not available!\n")
sys.exit()
options.version = "customized"
sys.stdout.write("Use local database: " + options.use_local)
sys.stdout.write("Use local database: " + options.use_local + "\n")
else:
if options.update:
options.version = "latest"
Expand Down Expand Up @@ -238,6 +240,14 @@ def rm_files(path_to, file_name_prefix="", file_name_postfix=""):
os.remove(os.path.join(path_to, file_to_del))


def find_version(organelle_type, hash_val, DB_dict, default_version_val="customized"):
for try_version in sorted(DB_dict, reverse=True):
if organelle_type in DB_dict[try_version] and hash_val == DB_dict[try_version][organelle_type]["sha256"]:
return try_version
else:
return default_version_val


def initialize_notation_database(which_blast, fasta_f, overwrite=False):
# blast index
output_base = remove_db_postfix(fasta_f)
Expand Down Expand Up @@ -332,17 +342,21 @@ def main():
sys.stdout.write("Warning: " + update_to_fa + " not available!\n")
else:
new_hash_val = cal_f_sha256(update_to_fa)
if new_hash_val != existing_seed_db[sub_o_type]["sha256"]: # match existed
for try_version in sorted(SEED_DB_HASH, reverse=True):
if new_hash_val == SEED_DB_HASH[try_version][sub_o_type]["sha256"]:
existing_seed_db[sub_o_type] = {"version": try_version, "sha256": new_hash_val}
else:
existing_seed_db[sub_o_type] = {"version": "customized", "sha256": new_hash_val}
if new_hash_val != existing_seed_db[sub_o_type]["sha256"]:
# for try_version in sorted(SEED_DB_HASH, reverse=True):
# if sub_o_type in SEED_DB_HASH[try_version] and \
# new_hash_val == SEED_DB_HASH[try_version][sub_o_type]["sha256"]:
# existing_seed_db[sub_o_type] = {"version": try_version, "sha256": new_hash_val}
# else:
# existing_seed_db[sub_o_type] = {"version": "customized", "sha256": new_hash_val}
existing_seed_db[sub_o_type] = \
{"version": find_version(sub_o_type, new_hash_val, SEED_DB_HASH),
"sha256": new_hash_val}
if os.path.realpath(os.path.split(update_to_fa)[0]) != os.path.realpath(_SEQ_DB_PATH):
copy(update_to_fa, _SEQ_DB_PATH)
initialize_seed_database(which_bowtie2=options.which_bowtie2,
fasta_f=target_output, overwrite=True)
else:
else: # match existed
# sys.stdout.write("The same " + sub_o_type + " Seed Database exists. Skipped.\n")
initialize_seed_database(which_bowtie2=options.which_bowtie2,
fasta_f=target_output, overwrite=False)
Expand Down Expand Up @@ -379,12 +393,16 @@ def main():
else:
new_hash_val = cal_f_sha256(update_to_fa)
if new_hash_val != existing_label_db[sub_o_type]["sha256"]: # match existed
for try_version in sorted(LABEL_DB_HASH, reverse=True):
if new_hash_val == LABEL_DB_HASH[try_version][sub_o_type]["sha256"]:
existing_label_db[sub_o_type] = {"version": try_version,
"sha256": new_hash_val}
else:
existing_label_db[sub_o_type] = {"version": "customized", "sha256": new_hash_val}
# for try_version in sorted(LABEL_DB_HASH, reverse=True):
# if sub_o_type in LABEL_DB_HASH[try_version] and \
# new_hash_val == LABEL_DB_HASH[try_version][sub_o_type]["sha256"]:
# existing_label_db[sub_o_type] = {"version": try_version,
# "sha256": new_hash_val}
# else:
# existing_label_db[sub_o_type] = {"version": "customized", "sha256": new_hash_val}
existing_label_db[sub_o_type] = \
{"version": find_version(sub_o_type, new_hash_val, LABEL_DB_HASH),
"sha256": new_hash_val}
if os.path.realpath(os.path.split(update_to_fa)[0]) != os.path.realpath(_LBL_DB_PATH):
copy(update_to_fa, _LBL_DB_PATH)
initialize_notation_database(which_blast=options.which_blast,
Expand Down Expand Up @@ -424,11 +442,14 @@ def main():
sys.stdout.write("Warning: " + update_to_fa + " not available!\n")
else:
new_hash_val = cal_f_sha256(update_to_fa)
for try_version in sorted(SEED_DB_HASH, reverse=True):
if new_hash_val == SEED_DB_HASH[try_version][sub_o_type]["sha256"]:
existing_seed_db[sub_o_type] = {"version": try_version, "sha256": new_hash_val}
else:
existing_seed_db[sub_o_type] = {"version": "customized", "sha256": new_hash_val}
# for try_version in sorted(SEED_DB_HASH, reverse=True):
# if sub_o_type in SEED_DB_HASH[try_version] and \
# new_hash_val == SEED_DB_HASH[try_version][sub_o_type]["sha256"]:
# existing_seed_db[sub_o_type] = {"version": try_version, "sha256": new_hash_val}
# else:
# existing_seed_db[sub_o_type] = {"version": "customized", "sha256": new_hash_val}
existing_seed_db[sub_o_type] = \
{"version": find_version(sub_o_type, new_hash_val, SEED_DB_HASH), "sha256": new_hash_val}
if os.path.realpath(os.path.split(update_to_fa)[0]) != os.path.realpath(_SEQ_DB_PATH):
copy(update_to_fa, _SEQ_DB_PATH)
initialize_seed_database(which_bowtie2=options.which_bowtie2,
Expand Down Expand Up @@ -456,12 +477,15 @@ def main():
sys.stdout.write("Warning: " + update_to_fa + " not available!\n")
else:
new_hash_val = cal_f_sha256(update_to_fa)
for try_version in sorted(LABEL_DB_HASH, reverse=True):
if new_hash_val == LABEL_DB_HASH[try_version][sub_o_type]["sha256"]:
existing_label_db[sub_o_type] = {"version": try_version,
"sha256": new_hash_val}
else:
existing_label_db[sub_o_type] = {"version": "customized", "sha256": new_hash_val}
# for try_version in sorted(LABEL_DB_HASH, reverse=True):
# if sub_o_type in LABEL_DB_HASH[try_version] and \
# new_hash_val == LABEL_DB_HASH[try_version][sub_o_type]["sha256"]:
# existing_label_db[sub_o_type] = {"version": try_version,
# "sha256": new_hash_val}
# else:
# existing_label_db[sub_o_type] = {"version": "customized", "sha256": new_hash_val}
existing_label_db[sub_o_type] = \
{"version": find_version(sub_o_type, new_hash_val, LABEL_DB_HASH), "sha256": new_hash_val}
if os.path.realpath(os.path.split(update_to_fa)[0]) != os.path.realpath(_LBL_DB_PATH):
copy(update_to_fa, _LBL_DB_PATH)
initialize_notation_database(which_blast=options.which_blast,
Expand Down

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