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Autodownload org codes #13

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Autodownload org codes #13

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7370ab5
changed it to autodownload it file does not exist
PelzKo Jan 6, 2025
2684b73
removed tester
PelzKo Jan 6, 2025
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27 changes: 21 additions & 6 deletions KEGGutils/KEGGapi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -986,6 +986,7 @@ def get_organism_codes(force_download=False):
org_filename = "organism_code_list"

org_codes = []
org_codespath = RES_PATH.joinpath("org_codes.txt")

if force_download:
organism_fulltext = download_textfile(
Expand All @@ -997,13 +998,27 @@ def get_organism_codes(force_download=False):
org_codes.append(kegg_code)

else:
org_codespath = RES_PATH.joinpath("org_codes.txt")
# with open("./res/org_codes.txt", "r+") as org_file:
# organism_fulltext = org_file.read()
organism_fulltext = org_codespath.read_text()
# Check if file exists. if it does not, download it and save it
if not os.path.exists(org_codespath):
if not os.path.isdir(RES_PATH):
os.mkdir(RES_PATH)

for line in organism_fulltext.splitlines():
org_codes.append(line)
organism_fulltext = download_textfile(
org_url, org_filename, verbose=False, force_download=force_download
)
for line in organism_fulltext.splitlines():
_, kegg_code, _, _ = line.strip().split("\t")
org_codes.append(kegg_code)

with open(org_codespath, "w") as f:
f.write('\n'.join(org_codes))
else:
# with open("./res/org_codes.txt", "r+") as org_file:
# organism_fulltext = org_file.read()
organism_fulltext = org_codespath.read_text()

for line in organism_fulltext.splitlines():
org_codes.append(line)

return org_codes

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