Cannot update Ensembl release #269
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Sorry for the long delay, checking this out now. |
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Reproduced on my machine:
Probably there's some new cat reference since release 107, going to check that out on Ensembl now. |
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OK, should work as of the code I just pushed: I'll get it on to PyPI later tonight (after unit tests finish on Travis) |
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Hi Alex,
No worries - thanks for the update. A quick follow up - do you envision in the future adding other model organisms into pyensembl? Such as Drosophila?
Thanks a lot!
Damian
… On Dec 1, 2022, at 6:08 PM, Alex Rubinsteyn ***@***.***> wrote:
OK, should work as of the code I just pushed:
➜ ~ pyensembl install --species cat --release 107
2022-12-01 18:07:04,482 - pyensembl.shell - INFO - Running 'install' for EnsemblRelease(release=107, species='felis_catus')
2022-12-01 18:07:04,482 - pyensembl.download_cache - INFO - Fetching /Users/iskander/Library/Caches/pyensembl/Felis_catus_9.0/ensembl107/Felis_catus.Felis_catus_9.0.107.gtf.gz from URL https://ftp.ensembl.org/pub/release-107/gtf/felis_catus/Felis_catus.Felis_catus_9.0.107.gtf.gz
I'll get it on to PyPI later tonight (after unit tests finish on Travis)
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Sure! Since they require a little curation to the ftp paths right, I'm
doing them one at a time as people request it. Which organisms do you need?
…On Thu, Dec 8, 2022, 10:09 AM DDudka9 ***@***.***> wrote:
Hi Alex,
No worries - thanks for the update. A quick follow up - do you envision in
the future adding other model organisms into pyensembl? Such as Drosophila?
Thanks a lot!
Damian
> On Dec 1, 2022, at 6:08 PM, Alex Rubinsteyn ***@***.***> wrote:
>
>
> OK, should work as of the code I just pushed:
>
> ➜ ~ pyensembl install --species cat --release 107
> 2022-12-01 18:07:04,482 - pyensembl.shell - INFO - Running 'install' for
EnsemblRelease(release=107, species='felis_catus')
> 2022-12-01 18:07:04,482 - pyensembl.download_cache - INFO - Fetching
/Users/iskander/Library/Caches/pyensembl/Felis_catus_9.0/ensembl107/Felis_catus.Felis_catus_9.0.107.gtf.gz
from URL
https://ftp.ensembl.org/pub/release-107/gtf/felis_catus/Felis_catus.Felis_catus_9.0.107.gtf.gz
> I'll get it on to PyPI later tonight (after unit tests finish on Travis)
>
> —
> Reply to this email directly, view it on GitHub <
#269 (comment)>,
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<#269 (comment)>,
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Nice! I am actually working on a computational pipeline that is used to detect positive selection in model organisms (which I am submitting soon). The pipeline is using pyensembl to generate input for an array of molecular evolution tools. I would be very excited if you could add Drosophila melanogaster and C. elegans. Along these lines, how do I cite pyensembl?
Thanks a lot - I appreciate you maintaining pyensembl - such a useful tool!
Best,
Damian
… On Dec 8, 2022, at 10:20 AM, Alex Rubinsteyn ***@***.***> wrote:
Sure! Since they require a little curation to the ftp paths right, I'm
doing them one at a time as people request it. Which organisms do you need?
On Thu, Dec 8, 2022, 10:09 AM DDudka9 ***@***.***> wrote:
> Hi Alex,
>
> No worries - thanks for the update. A quick follow up - do you envision in
> the future adding other model organisms into pyensembl? Such as Drosophila?
>
> Thanks a lot!
>
> Damian
>
>
>
> > On Dec 1, 2022, at 6:08 PM, Alex Rubinsteyn ***@***.***> wrote:
> >
> >
> > OK, should work as of the code I just pushed:
> >
> > ➜ ~ pyensembl install --species cat --release 107
> > 2022-12-01 18:07:04,482 - pyensembl.shell - INFO - Running 'install' for
> EnsemblRelease(release=107, species='felis_catus')
> > 2022-12-01 18:07:04,482 - pyensembl.download_cache - INFO - Fetching
> /Users/iskander/Library/Caches/pyensembl/Felis_catus_9.0/ensembl107/Felis_catus.Felis_catus_9.0.107.gtf.gz
> from URL
> https://ftp.ensembl.org/pub/release-107/gtf/felis_catus/Felis_catus.Felis_catus_9.0.107.gtf.gz
> > I'll get it on to PyPI later tonight (after unit tests finish on Travis)
> >
> > —
> > Reply to this email directly, view it on GitHub <
> #269 (comment)>,
> or unsubscribe <
> https://github.com/notifications/unsubscribe-auth/ATJLCITRNVBEZZZKLAODEL3WLEVWRANCNFSM57QMCXTQ
> >.
> > You are receiving this because you authored the thread.
> >
>
> —
> Reply to this email directly, view it on GitHub
> <#269 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAAL2OL26AGM3LI5Z4X3CH3WMH23FANCNFSM57QMCXTQ>
> .
> You are receiving this because you commented.Message ID:
> ***@***.***>
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I use pyensembl on daily bases and I love it! However, recently I noticed that I am not able to update Ensembl release from 90 to 107 (latest) for cat (error message attached below). I also see that the assembly that pyensembl is looking for (Felis_catus_6.2) does not match the current Ensembl release (Felis_catus_9.0).
When I try to update to 107:
I get this error:
Downloading ftp://ftp.ensembl.org/pub/release-107/gtf/felis_catus/Felis_catus.Felis_catus_6.2.107.gtf.gz to /Users/damian/Library/Caches/pyensembl/Felis_catus_6.2/ensembl107/Felis_catus.Felis_catus_6.2.107.gtf.gz
Traceback (most recent call last):
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/urllib/request.py", line 2450, in retrfile
self.ftp.cwd(file)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/ftplib.py", line 631, in cwd
return self.voidcmd(cmd)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/ftplib.py", line 278, in voidcmd
return self.voidresp()
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/ftplib.py", line 251, in voidresp
resp = self.getresp()
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/ftplib.py", line 246, in getresp
raise error_perm(resp)
ftplib.error_perm: 550 Failed to change directory.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/urllib/request.py", line 1573, in ftp_open
fp, retrlen = fw.retrfile(file, type)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/urllib/request.py", line 2452, in retrfile
raise URLError('ftp error: %r' % reason) from reason
urllib.error.URLError: <urlopen error ftp error: error_perm('550 Failed to change directory.')>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/damian/PycharmProjects/Freeda_pyinstaller_04_29_2022/freeda_pipeline.py", line 375, in
codon_frequencies=args.codon_frequencies, excluded_species=args.excluded_species)
File "/Users/damian/PycharmProjects/Freeda_pyinstaller_04_29_2022/freeda_pipeline.py", line 203, in freeda_pipeline
biotype, all_genes_ensembl = input_extractor.generate_ref_genome_object(wdir, ref_species)
File "/Users/damian/PycharmProjects/Freeda_pyinstaller_04_29_2022/freeda/input_extractor.py", line 379, in generate_ref_genome_object
ensembl.download() # this is suppose to bypass installing the release from outside python
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/site-packages/pyensembl/genome.py", line 266, in download
self._set_local_paths(download_if_missing=True, overwrite=overwrite)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/site-packages/pyensembl/genome.py", line 224, in _set_local_paths
overwrite=overwrite)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/site-packages/pyensembl/genome.py", line 188, in _get_gtf_path
overwrite=overwrite)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/site-packages/pyensembl/genome.py", line 181, in _get_cached_path
overwrite=overwrite)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/site-packages/pyensembl/download_cache.py", line 312, in local_path_or_install_error
overwrite=overwrite)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/site-packages/pyensembl/download_cache.py", line 288, in download_or_copy_if_necessary
overwrite)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/site-packages/pyensembl/download_cache.py", line 234, in _download_if_necessary
timeout=3600)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/site-packages/datacache/download.py", line 110, in _download_and_decompress_if_necessary
use_wget_if_available=use_wget_if_available)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/site-packages/datacache/download.py", line 68, in _download_to_temp_file
download_using_python()
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/site-packages/datacache/download.py", line 65, in download_using_python
_download(download_url, timeout=timeout))
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/site-packages/datacache/download.py", line 42, in _download
response = urllib.request.urlopen(req, data=None, timeout=timeout)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/urllib/request.py", line 1584, in ftp_open
raise exc.with_traceback(sys.exc_info()[2])
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/urllib/request.py", line 1573, in ftp_open
fp, retrlen = fw.retrfile(file, type)
File "/Users/damian/anaconda3/envs/py37/lib/python3.7/urllib/request.py", line 2452, in retrfile
raise URLError('ftp error: %r' % reason) from reason
urllib.error.URLError: <urlopen error ftp error: URLError("ftp error: error_perm('550 Failed to change directory.')")>
Thank you for maintaining the package!
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