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Fix dbcan download urls #77

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Merged
nextgenusfs merged 2 commits into from
Jun 21, 2026
Merged

Fix dbcan download urls #77

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2437865
fix: replace unstable dbCAN URLs with AWS S3 mirror and local metadat…
Jun 21, 2026
aae68f5
style: overwrite with exact binary-matching copies from verified loca…
Jun 21, 2026
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6 changes: 3 additions & 3 deletions funannotate2/downloads.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@
"uniprot": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz",
"uniprot-release": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt",
"merops": "https://ftp.ebi.ac.uk/pub/databases/merops/current_release/meropsscan.lib",
"dbCAN": "https://pro.unl.edu/dbCAN2/download/Databases/V14/dbCAN-HMMdb-V14.txt",
"dbCAN-tsv": "https://pro.unl.edu/dbCAN2/download/Databases/V12/CAZyDB.08062022.fam-activities.txt",
"dbCAN-log": "https://pro.unl.edu/dbCAN2/download/Databases/V11/readme.txt",
"dbCAN": "https://dbcan.s3.us-west-2.amazonaws.com/db_v5-2-9_5-5-2026/dbCAN.hmm",
"dbCAN-tsv": "https://raw.githubusercontent.com/nextgenusfs/funannotate2/main/funannotate2/resources/dbCAN-fam-HMMs.txt",
"dbCAN-log": "https://raw.githubusercontent.com/nextgenusfs/funannotate2/main/funannotate2/resources/dbCAN.changelog.txt",
"pfam": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz",
"pfam-tsv": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz",
"pfam-log": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam.version.gz",
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6 changes: 3 additions & 3 deletions funannotate2/downloads_v2.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@
"uniprot": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz",
"uniprot-release": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt",
"merops": "https://ftp.ebi.ac.uk/pub/databases/merops/current_release/meropsscan.lib",
"dbCAN": "https://pro.unl.edu/dbCAN2/download/Databases/V14/dbCAN-HMMdb-V14.txt",
"dbCAN-tsv": "https://pro.unl.edu/dbCAN2/download/Databases/V12/CAZyDB.08062022.fam-activities.txt",
"dbCAN-log": "https://pro.unl.edu/dbCAN2/download/Databases/V11/readme.txt",
"dbCAN": "https://dbcan.s3.us-west-2.amazonaws.com/db_v5-2-9_5-5-2026/dbCAN.hmm",
"dbCAN-tsv": "https://raw.githubusercontent.com/nextgenusfs/funannotate2/main/funannotate2/resources/dbCAN-fam-HMMs.txt",
"dbCAN-log": "https://raw.githubusercontent.com/nextgenusfs/funannotate2/main/funannotate2/resources/dbCAN.changelog.txt",
"pfam": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz",
"pfam-tsv": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz",
"pfam-log": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam.version.gz",
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23 changes: 20 additions & 3 deletions funannotate2/install.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ def install(args):
logger.info("Retrieving download links from GitHub Repo")
DBURL = json.loads(
requests.get(
"https://raw.githubusercontent.com/nextgenusfs/funannotate2/master/funannotate2/downloads_v2.json"
"https://raw.githubusercontent.com/nextgenusfs/funannotate2/main/funannotate2/downloads_v2.json"
).text
)["downloads"]
except: # noqa: E722
Expand Down Expand Up @@ -537,8 +537,25 @@ def dbCANDB(wget=False):
md5 = calcmd5remote(DBURL.get("dbCAN"))
# download data
download(DBURL.get("dbCAN"), hmm, wget=wget)
download(DBURL.get("dbCAN-tsv"), familyinfo, wget=wget)
download(DBURL.get("dbCAN-log"), versionfile, wget=wget)

# Try to copy familyinfo and versionfile from local package resources, fallback to download
local_resources_dir = os.path.join(os.path.dirname(__file__), "resources")
local_fam = os.path.join(local_resources_dir, "dbCAN-fam-HMMs.txt")
local_changelog = os.path.join(local_resources_dir, "dbCAN.changelog.txt")

if os.path.exists(local_fam) and os.path.exists(local_changelog):
import shutil
try:
shutil.copy(local_fam, familyinfo)
shutil.copy(local_changelog, versionfile)
logger.info("Copied dbCAN metadata files from package resources")
except Exception as e:
logger.warning(f"Could not copy local metadata resources ({e}), falling back to download")
download(DBURL.get("dbCAN-tsv"), familyinfo, wget=wget)
download(DBURL.get("dbCAN-log"), versionfile, wget=wget)
else:
download(DBURL.get("dbCAN-tsv"), familyinfo, wget=wget)
download(DBURL.get("dbCAN-log"), versionfile, wget=wget)
dbdate = ""
dbvers = ""
with io.open(versionfile, encoding="utf8", errors="ignore") as infile:
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