chiangtw
commented
1 year ago Hi Migle,
Thanks for the feedback on CircMiMi package!
This bug is due to the annotation GTF file from Ensembl 75, which not having the "transcript_biotype" attribute for "transcript". You may try the GTF file from Gencode v19 instead, it should be work nicely.
We would fix this bug in the near future.
Best, tw
Dear developers,
Thanks for creating CircMiMi, it's an easy to use and very useful tool. However, I am having problems creating an hg19 reference genome instead of hg38. I get the following error: `circmimi_tools genref --species hsa --source ensembl --version 75 refs/ --2022-11-09 12:05:13-- ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz => './Homo_sapiens.GRCh37.75.gtf.gz' Resolving ftp.ensembl.org (ftp.ensembl.org)... 193.62.193.139 Connecting to ftp.ensembl.org (ftp.ensembl.org)|193.62.193.139|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/release-75/gtf/homo_sapiens ... done. ==> SIZE Homo_sapiens.GRCh37.75.gtf.gz ... 39344043 ==> PASV ... done. ==> RETR Homo_sapiens.GRCh37.75.gtf.gz ... done. Length: 39344043 (38M) (unauthoritative)
Homo_sapiens.GRCh37.75.gtf.gz 100%[=================================================>] 37.52M 33.3MB/s in 1.1s
2022-11-09 12:05:15 (33.3 MB/s) - './Homo_sapiens.GRCh37.75.gtf.gz' saved [39344043]
--2022-11-09 12:05:15-- ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz => './Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz' Resolving ftp.ensembl.org (ftp.ensembl.org)... 193.62.193.139 Connecting to ftp.ensembl.org (ftp.ensembl.org)|193.62.193.139|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/release-75/fasta/homo_sapiens/dna ... done. ==> SIZE Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz ... 869930767 ==> PASV ... done. ==> RETR Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz ... done. Length: 869930767 (830M) (unauthoritative)
Homo_sapiens.GRCh37.75.dna.pri 100%[=================================================>] 829.63M 45.3MB/s in 27s
2022-11-09 12:05:43 (30.4 MB/s) - './Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz' saved [869930767]
--2022-11-09 12:05:43-- ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.75.cdna.all.fa.gz => './Homo_sapiens.GRCh37.75.cdna.all.fa.gz' Resolving ftp.ensembl.org (ftp.ensembl.org)... 193.62.193.139 Connecting to ftp.ensembl.org (ftp.ensembl.org)|193.62.193.139|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/release-75/fasta/homo_sapiens/cdna ... done. ==> SIZE Homo_sapiens.GRCh37.75.cdna.all.fa.gz ... 60646070 ==> PASV ... done. ==> RETR Homo_sapiens.GRCh37.75.cdna.all.fa.gz ... done. Length: 60646070 (58M) (unauthoritative)
Homo_sapiens.GRCh37.75.cdna.al 100%[=================================================>] 57.84M 33.5MB/s in 1.7s
2022-11-09 12:05:46 (33.5 MB/s) - './Homo_sapiens.GRCh37.75.cdna.all.fa.gz' saved [60646070]
--2022-11-09 12:05:46-- ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh37.75.ncrna.fa.gz => './Homo_sapiens.GRCh37.75.ncrna.fa.gz' Resolving ftp.ensembl.org (ftp.ensembl.org)... 193.62.193.139 Connecting to ftp.ensembl.org (ftp.ensembl.org)|193.62.193.139|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/release-75/fasta/homo_sapiens/ncrna ... done. ==> SIZE Homo_sapiens.GRCh37.75.ncrna.fa.gz ... 7735481 ==> PASV ... done. ==> RETR Homo_sapiens.GRCh37.75.ncrna.fa.gz ... done. Length: 7735481 (7.4M) (unauthoritative)
Homo_sapiens.GRCh37.75.ncrna.f 100%[=================================================>] 7.38M 12.3MB/s in 0.6s
2022-11-09 12:05:47 (12.3 MB/s) - './Homo_sapiens.GRCh37.75.ncrna.fa.gz' saved [7735481]
Traceback (most recent call last): File "/Users/migab/miniconda3/envs/circmimi/bin/circmimi_tools", line 8, in
sys.exit(cli())
File "/Users/migab/miniconda3/envs/circmimi/lib/python3.10/site-packages/click/core.py", line 1130, in call
return self.main(args, kwargs)
File "/Users/migab/miniconda3/envs/circmimi/lib/python3.10/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/Users/migab/miniconda3/envs/circmimi/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/migab/miniconda3/envs/circmimi/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/Users/migab/miniconda3/envs/circmimi/lib/python3.10/site-packages/click/core.py", line 760, in invoke
return __callback(args, **kwargs)
File "/Users/migab/miniconda3/envs/circmimi/lib/python3.10/site-packages/circmimi/scripts/circmimi_tools.py", line 164, in generate_references
info, ref_files = genref.generate(species, source, version, ref_dir)
File "/Users/migab/miniconda3/envs/circmimi/lib/python3.10/site-packages/circmimi/reference/genref.py", line 311, in generate
anno_ref.generate()
File "/Users/migab/miniconda3/envs/circmimi/lib/python3.10/site-packages/circmimi/reference/genref.py", line 26, in generate
gendb.generate(self.src_name, self.filename)
File "/Users/migab/miniconda3/envs/circmimi/lib/python3.10/site-packages/circmimi/reference/gendb.py", line 193, in generate
tables_raw_data.parse(gtf_path)
File "/Users/migab/miniconda3/envs/circmimi/lib/python3.10/site-packages/circmimi/reference/gendb.py", line 113, in parse
biotypes = sorted(set(map(itemgetter(2), genes + transcripts)))
TypeError: '<' not supported between instances of 'NoneType' and 'str'`
Could you help me with fixing this issue?
Best wishes, Migle