hg19 reference genome bug

[MigleSur]

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

[chiangtw]

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