pachterlab / gget Goto Github PK
View Code? Open in Web Editor NEW🧬 gget enables efficient querying of genomic reference databases
Home Page: https://gget.bio
License: BSD 2-Clause "Simplified" License
🧬 gget enables efficient querying of genomic reference databases
Home Page: https://gget.bio
License: BSD 2-Clause "Simplified" License
Hi Laura,
It would be great if there was an option to be able to submit a MSA instead of a protein sequence as input for gget alphafold. The use case here is to submit (manually) curated MSA, instead of "all" sequences holomologs that come usually with sequence errors (prediction errors, isoforms, fragments... etc; PMID: 33172385), inorder to improve the folding predictions.
uswest.ensembl.org was discontinued. Change URLs returned by gget search to useast.ensembl.org
NA
Not applicable
Not applicable
Not applicable
No response
No response
i have used example sequence in the alphafold module and it works fine however when I give it a custom sequence it give the said error
Keyerror: "0000:query".
Please can you guide regarding the matter
Encountered error using blast function in gget via pip install without an existing lxml installation. Would adding lxml to dependencies in requirements.txt correct this?
Many thanks for this brilliant tool. I was wondering if it would be possible to add the "subcellular localisation" segment of the uniprot ID to the tools output?
This would be immensely helpful in terms of filtering for sub cellular location.
Many thanks and apologies if it does this already, but I couldn't identify this data in the output
I am able to use every gget module except for the alphaFold module. Whenever I implement a command line with AlphaFold the Jupyter Notebook kernel dies almost immediately. Is this something that occurs for others? Any recommendations are appreciated.
import gget
gget.setup("alphafold")
gget.alphafold("MAAHKGAEH")
We want to use gget.muscle for multiple sequence alignments for multiple species. These multiple species have different length ensembl_id/gene_names. Therefore, they start at different places on the page.
I import gget into Google CoLab each time I run my analysis. For this example it is only minimal in other cases it can be more severe depending on the species.
Windows, Other (please specify above)
Google Colab (please include a shareable link above)
Not M1
!pip install --upgrade gget
import gget
gget.search
gget.seq
gget.muscle
No response
Hi,
I am searching for the gene "WISP2" using gget with the following command:
gget search -s homo_sapiens "WISP2"
which returns the following result:
Thu Jun 29 14:53:00 2023 INFO Fetching results from database: homo_sapiens_core_109_38 Thu Jun 29 14:53:02 2023 INFO Total matches found: 1. Thu Jun 29 14:53:02 2023 INFO Query time: 5.15 seconds. [ { "ensembl_id": "ENSG00000244558", "gene_name": "KCNK15-AS1", "ensembl_description": "KCNK15 and WISP2 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:49901]", "ext_ref_description": "KCNK15 and WISP2 antisense RNA 1", "biotype": "lncRNA", "url": "https://useast.ensembl.org/homo_sapiens/Gene/Summary?g=ENSG00000244558" } ]
But I would expect the gene with ensembl ID "ENSG00000064205" which has the symbol "CCN5" but lists "WISP2" as a synonym.
Apparently gget matches the search term in the "description" field but one can argue that a match in the "Gene Synonyms" field should be weighted higher.
0.27.7
Linux
Command-line
Not M1
gget search -s homo_sapiens "WISP2"
Output for the gene "ENSG00000244558" with symbol "KCNK15-AS1" but I would expect the gene "ENSG00000064205" with symbol "CCN5".
The reason is that the gene symbol "WISP2" (search term) is a gene synonym for "CCN5".
Thank you for the very cool and important package! This will save me hours and hours of computational work
I was wondering if you can add an option to BLAST two protein sequences against each other and get their e-value etc. I have a list of proteins that I want to compare to each other. If you'd prefer to point me to how I can make this feature and do a pull request, I'm more than happy to do so too!
The idea would to create a feature similar to gget search for Ensembl but also for UCSC IDs.
I remember the last time I had to do something similar, in the end I had to do a request to the path below where "{ucsc_id}" would be the ID itself:
"https://genome-euro.ucsc.edu/cgi-bin/hgGene?hgg_gene={ucsc_id}&db=hg19"
Links that should help:
https://genome.ucsc.edu/goldenPath/help/api.html
https://www.biotools.fr/human/ucsc_id_converter
Extension of existing module
The gget_cellxgene
module could support additional filtering options, providing the full set of metadata attributes that are available in the Census. In particular, supporting is_primary_data
will allow users to ignore cells that are duplicated across multiple CELLxGENE datasets. See https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/3.0.0/schema.md#is_primary_data. It would be reasonable to have a default value of True
for this attribute.
Also, the current defaults will attempt to load the entire Census into an AnnData object, which requires a considerable amount of RAM (100's GBs) and high network bandwidth. You might consider enforcing that at least one obs filter is specified or a subset of genes is specified.
No response
No response
Extension of existing module
I tried to use gget blast
and I noticed I can not filter by taxonomy. It would be nice if you can implement that. Here is the filter box in uniprot blast:
Looking at the result, this is the command option added to the blast run that may help:
-taxidlist ncbiblast-R20230405-025515-0636-88381305-p1m.taxidlist
No response
No response
Hello,
This request is to make the params of BLAST match exactly that of the web app (or an ability to pass them as xargs to the code)
This is an example of params sent by the code today:
Program | blastn |
Word size | 28 |
Expect value | 10 |
Hitlist size | 100 |
Match/Mismatch scores | 1,-2 |
Gapcosts | 0,2.5 |
Low Complexity Filter | Yes |
Filter string | L;m; |
Genetic Code | 1 |
and these are the params if BLAST is done on the web directly
Program | blastn |
---|---|
Word size | 11 |
Expect value | 0.05 |
Hitlist size | 100 |
Match/Mismatch scores | 2,-3 |
Gapcosts | 5,2 |
Low Complexity Filter | Yes |
Filter string | L;m; |
Genetic Code | 1 |
Thank you very much
i have used gget to predict the structure of chloride dismutase and it successfully gave me the pdb file of the structure in a monomeric form and when i cross checked it with pdb database it showed the structure to be a hexameric protein.
Now is it necessary to fill this gap ?
I love the new alphafold feature! Could there also be a gget pdb
command for fetching structures from PDB? Combined with gget blast -db pdbaa
this could be very powerful for comparing predictions and templates.
hello,
I installed gget using the command:
pip install --upgrade gget
then when i tried to install alphafold using the command:
gget setup alphafold
I got the following error:
gget setup alphafold
Traceback (most recent call last):
File "/home/najib/miniconda3/bin/gget", line 5, in <module>
from gget.main import main
File "/home/najib/miniconda3/lib/python3.9/site-packages/gget/__init__.py", line 10, in <module>
from .gget_alphafold import alphafold
File "/home/najib/miniconda3/lib/python3.9/site-packages/gget/gget_alphafold.py", line 31, in <module>
from ipywidgets import GridspecLayout
File "/home/najib/miniconda3/lib/python3.9/site-packages/ipywidgets/__init__.py", line 25, in <module>
from .widgets import *
File "/home/najib/miniconda3/lib/python3.9/site-packages/ipywidgets/widgets/__init__.py", line 4, in <module>
from .widget import Widget, CallbackDispatcher, register, widget_serialization
File "/home/najib/miniconda3/lib/python3.9/site-packages/ipywidgets/widgets/widget.py", line 13, in <module>
from ipykernel.comm import Comm
File "/home/najib/miniconda3/lib/python3.9/site-packages/ipykernel/comm/__init__.py", line 3, in <module>
from .comm import Comm
File "/home/najib/miniconda3/lib/python3.9/site-packages/ipykernel/comm/comm.py", line 14, in <module>
from ipykernel.kernelbase import Kernel
File "/home/najib/miniconda3/lib/python3.9/site-packages/ipykernel/kernelbase.py", line 70, in <module>
class Kernel(SingletonConfigurable):
File "/home/najib/miniconda3/lib/python3.9/site-packages/ipykernel/kernelbase.py", line 79, in Kernel
processes: t.Dict[str, psutil.Process] = {}
AttributeError: module 'psutil' has no attribute 'Process'
i uninstalled the psutil and installed again, i got the same error.
what is the possible solution?
thank you.
Hi,
when i uesd command gget pdb 1R42 -o 1R42.pdb, recieved error with
Traceback (most recent call last):
File "/home/xxx/anaconda3/envs/gmx_plumed/bin/gget", line 8, in
sys.exit(main())
File "/home/xxx/anaconda3/envs/gmx_plumed/lib/python3.8/site-packages/gget/main.py", line 2102, in main
pdb_results = pdb(
TypeError: pdb() got an unexpected keyword argument 'verbose'
0.27.7
Linux
Command-line
Not M1
gget pdb 1R42 -o 1R42.pdb
Traceback (most recent call last):
File "/home/xxx/anaconda3/envs/gmx_plumed/bin/gget", line 8, in <module>
sys.exit(main())
File "/home/xxx/anaconda3/envs/gmx_plumed/lib/python3.8/site-packages/gget/main.py", line 2102, in main
pdb_results = pdb(
TypeError: pdb() got an unexpected keyword argument 'verbose'
Extension of existing module
Dear Sir/Madame,
It would be highly beneficial if it will be possible to download only exons, when ask about sequences of all or particular isoform of mRNA. Now get download together with introns, unfortunately.
Best regards,
Iriną Tuszynska.
get seq -iso -exons
isoforms in fasta format without introns
Hi!
Would it be possible to specify a background set of genes for the enrichr
function?
Best
GJ
When running gget ref
in the biocontainer (quay.io/biocontainers/gget:0.27.2--pyhdfd78af_0, built automatically from conda) it fails because curl is not installed.
Solution:
Related to #53
0.27.2
Command-line
No response
Not M1
gget ref -d -w dna homo_sapiens
Wed Jan 25 15:21:53 2023 INFO Fetching reference information for homo_sapiens from Ensembl release: 108.
sh: curl: command not found
Hi!
I'm enquiring if it is planned to include support for AlphaFold multimer in a future release. Would be greatly appreciated!
Esa-Pekka
When I try to execute gget muscle via command line or via python script I get the same error message:
Via command line:
C:\Users\mypath > gget muscle fastas_test.txt
Or via python script:
file_name = "fastas_test.txt" gget.muscle(file_name) print(type(muscle_alignment)) print(muscle_alignment)
I get the same error message:
"Fri Aug 18 15:52:58 2023 INFO MUSCLE compiled.
Fri Aug 18 15:52:58 2023 INFO MUSCLE aligning...
Invalid command line
Expected -option_name or --option_name, got '-'"
This is how my fasta file is formatted:
Sequence1
MKTITLECMAIKLLDHLSEKEEQVKQRAEGEVKPEALQEALEKALKETGGVTVTKH
VRWTDGLTCGQLIKTNHPDKPTRIYVCLRGTKAKIADGAILKEDVIEKSTLNKFDLRG
ELKIEEKLRHLHPENSQSGDYPEAQIADGSKEVTLRQTCPTGWYFLRLLVDKDDKSYIK
ALAEKAAAKKVGELFNRYERPDCTLAKLDYVRVQVNIDAGGVLAALDRAEAIYALGLKA
ETEDGVVKLAADDKAAAPKAASRDPKAAGRVSSDPGVDSDGRGAPGPDGVGDSDSEDIAD
SEDKK
Sequence2
MSTQQIYTQVKVLQAMRHNGKLTLIIRATGGVVKLAADDKAAAPKAASRDPKAAGRVSS
DPGVDSDGRGAPGPDGVGDSDSEDIADSEDKK
0.27.0
Windows
Command-line
Not M1
gget muscle fastas_test.txt
Fri Aug 18 15:52:36 2023 INFO MUSCLE compiled.
Fri Aug 18 15:52:36 2023 INFO MUSCLE aligning...
Invalid command line
Expected -option_name or --option_name, got '-'
Hello,
Thanks for the great package. I think there may be intermittent issues with the UniProt connection, I received this error today:
But as you can see, there is a UniProt entry for this gene: https://www.uniprot.org/uniprot/Q8NBP7
Oddly, grabbing amino acid sequences worked fine for me yesterday. I appreciate any tips!
Hello, thank you for this great tool! I am having trouble with the gget setup alphafold command.
I created a conda environment with gget, git, pip and openmm=7.5.1 (attached). The first time I executed the setup command it finished with no errors, but when I tried to run gget.alphafold() it says "Some third-party dependencies are missing". Then, when I run the setup command again this is the error message:
Thu Jan 19 10:45:08 2023 INFO openmm v7.5.1 already installed.
Thu Jan 19 10:45:08 2023 INFO Installing AlphaFold from source (requires pip and git).
Note: switching to '569eb4fea3733b979cb0442750b875759dd5ecc0'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
ERROR: Ignored the following versions that require a different python version: 1.6.2 Requires-Python >=3.7,<3.10; 1.6.3 Requires-Python >=3.7,<3.10; 1.7.0 Requires-Python >=3.7,<3.10; 1.7.0rc1 Requires-Python >=3.7,<3.10; 1.7.0rc2 Requires-Python >=3.7,<3.10; 1.7.1 Requires-Python >=3.7,<3.10
ERROR: Could not find a version that satisfies the requirement scipy==1.7.0 (from versions: 0.8.0, 0.9.0, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.12.1, 0.13.0, 0.13.1, 0.13.2, 0.13.3, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.4.0, 1.4.1, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 1.5.4, 1.6.0, 1.6.1, 1.7.2, 1.7.3, 1.8.0rc1, 1.8.0rc2, 1.8.0rc3, 1.8.0rc4, 1.8.0, 1.8.1, 1.9.0rc1, 1.9.0rc2, 1.9.0rc3, 1.9.0, 1.9.1, 1.9.2, 1.9.3, 1.10.0rc1, 1.10.0rc2, 1.10.0)
ERROR: No matching distribution found for scipy==1.7.0
Thu Jan 19 10:46:34 2023 ERROR AlphaFold installation failed.
Thu Jan 19 10:46:34 2023 INFO openmm v7.5.1 already installed.
Thu Jan 19 10:46:34 2023 INFO Installing AlphaFold from source (requires pip and git).
Note: switching to '569eb4fea3733b979cb0442750b875759dd5ecc0'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
ERROR: Ignored the following versions that require a different python version: 1.6.2 Requires-Python >=3.7,<3.10; 1.6.3 Requires-Python >=3.7,<3.10; 1.7.0 Requires-Python >=3.7,<3.10; 1.7.0rc1 Requires-Python >=3.7,<3.10; 1.7.0rc2 Requires-Python >=3.7,<3.10; 1.7.1 Requires-Python >=3.7,<3.10
ERROR: Could not find a version that satisfies the requirement scipy==1.7.0 (from versions: 0.8.0, 0.9.0,
[alphafold_conda.txt](https://github.com/pachterlab/gget/files/10455613/alphafold_conda.txt)
0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.12.1, 0.13.0, 0.13.1, 0.13.2, 0.13.3, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.4.0, 1.4.1, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 1.5.4, 1.6.0, 1.6.1, 1.7.2, 1.7.3, 1.8.0rc1, 1.8.0rc2, 1.8.0rc3, 1.8.0rc4, 1.8.0, 1.8.1, 1.9.0rc1, 1.9.0rc2, 1.9.0rc3, 1.9.0, 1.9.1, 1.9.2, 1.9.3, 1.10.0rc1, 1.10.0rc2, 1.10.0)
ERROR: No matching distribution found for scipy==1.7.0
Thu Jan 19 10:47:04 2023 ERROR AlphaFold installation failed.
Thu Jan 19 10:47:05 2023 ERROR
Any suggestions on how to continue?
Hi! I am hitting a SSL cert problem when running alphafold setup:
Tue Aug 16 10:18:49 2022 INFO Downloading AlphaFold model parameters (requires 4.1 GB of storage). This might take a few minutes.
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: https://curl.se/docs/sslcerts.html
curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
Where are the parameters being downloaded from? I believe this will help me check if I have the right certs and are in the right place. Any additional advice to solve this error would be greatly appreciated! Thank you!
df_uniprot['gene_name']
is NaN (which is np.float
, gget_seq.py expects str
)ids where I encounter the error:
['ENSG00000275740', 'ENSG00000249624', 'ENSG00000288716', 'ENSG00000288712',
'ENSG00000288708', 'ENSG00000288706', 'ENSG00000288654', 'ENSG00000288646',
'ENSG00000288644', 'ENSG00000288634', 'ENSG00000288626', 'ENSG00000288625',
'ENSG00000288623', 'ENSG00000288608', 'ENSG00000288570', 'ENSG00000286224',
'ENSG00000286131', 'ENSG00000288629', 'ENSG00000288645', 'ENSG00000284934',
'ENSG00000284895', 'ENSG00000284684', 'ENSG00000285976', 'ENSG00000288715',
'ENSG00000257046']
0.27.9
Linux, macOS
Python
Not M1
import gget
gget.seq(['ENSG00000257046'], translate=True)
Thu Oct 12 18:16:04 2023 INFO Requesting amino acid sequence of the canonical transcript ENST00000540229 of gene ENSG00000257046 from UniProt.
Thu Oct 12 18:16:05 2023 WARNING No reviewed UniProt results were found for ID ENST00000540229. Returning all unreviewed results.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/fruity/miniconda3/envs/biopy/lib/python3.8/site-packages/gget/gget_seq.py", line 379, in seq
">"
TypeError: can only concatenate str (not "numpy.float64") to str
allow seqs to be lower case
latest
Not applicable
Not applicable
Not applicable
No response
No response
Hi @lauraluebbert ,
I noticed with gget 0.2.0 that gget --help
returns with an error code. Also, it appears that gget -v
or gget --version
aren't currently working as expected.
Best,
Mike
Extension of existing module
https://www.ncbi.nlm.nih.gov/books/NBK569856/
No response
No response
I cannot get the Alphafold module to work, as openmm v.7.5.1 is no longer available from conda-forge. Later versions of openmm do not have the version method, causing gget to crash using later versions.
Extension of existing module
Would be great to be able to query the Open Targets databases for interpreting genome variation and function via their API: https://platform.opentargets.org/api
No response
No response
Extension of existing module
Have gget fetch FASTAs and GTFs from GENCODE
No response
No response
Extension of existing module
Hi,
I would like to have the option to specify a version of the queried ensembl database when searching with the "search" module.
As far as I can see, gget uses the most current version but I can see use-cases where one would like to query older versions also.
gget search -s homo_sapiens -v 96 "ACE2"
No response
Hello,
I'm trying to run gget alphafold on my M1 mac, but am encountering the following error:
zsh: illegal hardware instruction
I noticed other threads (143) that comment on the difficulty of running tensorflow with m1 hardware and was wondering if this might be the issue?
I checked to see what version of tensorflow was installed with pip and found several tensorflow-related packages, but not tensorflow itself, I'm guessing this is why other workarounds don't work (i.e. installing tensorflow alpha, or what is suggested here: https://www.youtube.com/watch?v=WFIZn6titnc) :
tensorboard 2.9.1
tensorboard-data-server 0.6.1
tensorboard-plugin-wit 1.8.1
tensorflow-cpu 2.9.1
tensorflow-estimator 2.9.0
tensorflow-io-gcs-filesystem 0.26.0
Is there an easy way to resolve this?
-Alex
is there any way to export the generated plots as svg?
New module
Link to the API:
http://elm.eu.org/api/manual.html
No response
No response
Extension of existing module
This is a really useful easy-to-use package. I have been using this for relatively large requests and I was wondering if there is a way to reduce the verbosity of the logging info or turn off the logging completely?
No response
No response
Dear developers,
I found minor issue running gget alphafold on macOS (11.6.5). My terminal went blocked after finishing "Jackhmmer search". It was unblocked by closing the window of the image reporting the "Non-Gap Count" vs "Per-Residue Count Of Non-Gap Amin Acids in the MSA For Sequence 1". Then it proceeded with "Running model_2".
Best,
Lorenzo
Running:
gget.ref("mouse")
I've got this
error:
ConnectionResetError: [Errno 104] Connection reset by peer
During handling of the above exception, another exception occurred:
ProtocolError Traceback (most recent call last)
ProtocolError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
During handling of the above exception, another exception occurred:
ConnectionError Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/requests/adapters.py in send(self, request, stream, timeout, verify, cert, proxies)
496
497 except (ProtocolError, socket.error) as err:
--> 498 raise ConnectionError(err, request=request)
499
500 except MaxRetryError as e:
ConnectionError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
I have installed gget in my ubuntu 20.04. However, when I do a gget setup alphafold it sets it up fine as below:
Thu Jan 12 06:06:31 2023 INFO openmm v7.5.1 already installed.
Thu Jan 12 06:06:31 2023 INFO Installing AlphaFold from source (requires pip and git).
Thu Jan 12 06:06:37 2023 INFO AlphaFold installed succesfully.
Thu Jan 12 06:06:37 2023 INFO Installing pdbfixer from source (requires pip and git).
Thu Jan 12 06:06:41 2023 INFO pdbfixer installed succesfully.
Thu Jan 12 06:06:41 2023 INFO AlphaFold model parameters already downloaded.
However my run on
gget alphafold MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH
returns the following error. I have also tried doing pip install -U gget followed by pip install -U gget I still get the same error:
Traceback (most recent call last):
File "/home/sutripa/anaconda3/bin/pip", line 11, in
sys.exit(main())
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 70, in main
return command.main(cmd_args)
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 98, in main
return self._main(args)
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 214, in _main
self.handle_pip_version_check(options)
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 143, in handle_pip_version_check
session = self._build_session(
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 88, in _build_session
session = PipSession(
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_internal/network/session.py", line 289, in init
self.headers["User-Agent"] = user_agent()
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_internal/network/session.py", line 132, in user_agent
linux_distribution = distro.linux_distribution() # type: ignore
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_vendor/distro.py", line 125, in linux_distribution
return _distro.linux_distribution(full_distribution_name)
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_vendor/distro.py", line 681, in linux_distribution
self.version(),
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_vendor/distro.py", line 741, in version
self.lsb_release_attr('release'),
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_vendor/distro.py", line 903, in lsb_release_attr
return self._lsb_release_info.get(attribute, '')
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_vendor/distro.py", line 556, in get
ret = obj.dict[self._fname] = self._f(obj)
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/pip/_vendor/distro.py", line 1014, in _lsb_release_info
stdout = subprocess.check_output(cmd, stderr=devnull)
File "/home/sutripa/anaconda3/lib/python3.9/subprocess.py", line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/home/sutripa/anaconda3/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '('lsb_release', '-a')' returned non-zero exit status 1.
Traceback (most recent call last):
File "/home/sutripa/anaconda3/bin/gget", line 8, in
sys.exit(main())
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/gget/main.py", line 1551, in main
alphafold(
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/gget/gget_alphafold.py", line 302, in alphafold
from alphafold.model import model
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/alphafold/model/model.py", line 20, in
from alphafold.model import features
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/alphafold/model/features.py", line 19, in
from alphafold.model.tf import input_pipeline
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/alphafold/model/tf/input_pipeline.py", line 17, in
from alphafold.model.tf import data_transforms
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/alphafold/model/tf/data_transforms.py", line 18, in
from alphafold.model.tf import shape_helpers
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/alphafold/model/tf/shape_helpers.py", line 16, in
import tensorflow.compat.v1 as tf
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/tensorflow/init.py", line 51, in
from ._api.v2 import compat
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/tensorflow/_api/v2/compat/init.py", line 37, in
from . import v1
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/init.py", line 30, in
from . import compat
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/compat/init.py", line 37, in
from . import v1
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/compat/v1/init.py", line 47, in
from tensorflow._api.v2.compat.v1 import lite
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/lite/init.py", line 9, in
from . import experimental
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/lite/experimental/init.py", line 8, in
from . import authoring
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/lite/experimental/authoring/init.py", line 8, in
from tensorflow.lite.python.authoring.authoring import compatible
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/tensorflow/lite/python/authoring/authoring.py", line 43, in
from tensorflow.lite.python import convert
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/tensorflow/lite/python/convert.py", line 28, in
from tensorflow.lite.python import util
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/tensorflow/lite/python/util.py", line 55, in
from jax import xla_computation as _xla_computation
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/jax/init.py", line 35, in
from jax import config as _config_module
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/jax/config.py", line 17, in
from jax._src.config import config # noqa: F401
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/jax/_src/config.py", line 27, in
from jax._src import lib
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/jax/_src/lib/init.py", line 74, in
version = check_jaxlib_version(
File "/home/sutripa/anaconda3/lib/python3.9/site-packages/jax/_src/lib/init.py", line 69, in check_jaxlib_version
raise RuntimeError(msg)
RuntimeError: jaxlib version 0.4.1 is newer than and incompatible with jax version 0.3.25. Please update your jax and/or jaxlib packages.
Extension of existing module
Dear Devs,
Hi! I really like this package, it’s a great project, but I ran into an issue when I added it to a workflow; I need to process a large number of Ensembl IDs so get.info would be the perfect fit for that but it takes a rather long time for mouse Ensembl IDs and it seems like that’s entirely due to the PDB API (which in my case, currently with mouse IDs, only returns NaNs). Would it be possible to make the PDB search mutable? I’m currently doing in that in a modified version of this function and like that it takes 5 s rather than 2.5 min per call.
Best,
Matthias
gget.info('ENSexampleID', pdb=False)
Same as usual but without PDB entry (or NaN instead of an entry)
Dear developers,
I tried to run alphafold from the gget package and compare the execution times to the Alphafold2 implemented in Google Colab.
I submitted the following sequence and used the default parameters in both cases: MAEHGAHFTAASVADDQPSIFEVVAQDSLMTAVRPALQHVVKVLAESNPTHYGFLWRWFDEIFTLLDLLLQQHYLSRTSASFSENFYGLKRIVMGDTHKSQRLASAGLPKQQLWKSIMFLVLLPYLKVKLEKLVSSLREEDEYSIHPPSSRWKRFYRAFLAAYPFVNMAWEGWFLVQQLRYILGKAQHHSPLLRLAGVQLGRLTVQDIQALEHKPAKASMMQQPARSVSEKINSALKKAVGGVALSLSTGLSVGVFFLQFLDWWYSSENQETIKSLTALPTPPPPVHLDYNSDSPLLPKMKTVCPLCRKTRVNDTVLA
The Colab AlphaFold finished in 15 minutes and required 4.6GB RAM and 3.6GB of GPU while gget AlphaFold finished in ~5h in a desktop computer with 8GB GPU, and 64GB RAM.
If I understood correctly, gget alphafold implements the simplified Alphafold version that also uses Google Colab. Why is there such a great difference in execution time?
0.27.2
Linux
Command-line
Not M1
gget alphafold MAEHGAHFTAASVADDQPSIFEVVAQDSLMTAVRPALQHVVKVLAESNPTHYGFLWRWFDEIFTLLDLLLQQHYLSRTSASFSENFYGLKRIVMGDTHKSQRLASAGLPKQQLWKSIMFLVLLPYLKVKLEKLVSSLREEDEYSIHPPSSRWKRFYRAFLAAYPFVNMAWEGWFLVQQLRYILGKAQHHSPLLRLAGVQLGRLTVQDIQALEHKPAKASMMQQPARSVSEKINSALKKAVGGVALSLSTGLSVGVFFLQFLDWWYSSENQETIKSLTALPTPPPPVHLDYNSDSPLLPKMKTVCPLCRKTRVNDTVLA
No response
Installed on host via pip install --upgrade gget
:
$ system_profiler SPSoftwareDataType SPHardwareDataType
Software:
System Software Overview:
System Version: macOS 12.5 (21G72)
Kernel Version: Darwin 21.6.0
Boot Volume: Macintosh HD
Boot Mode: Normal
Computer Name: Earl Grey
User Name: Alex Reynolds (areynolds)
Secure Virtual Memory: Enabled
System Integrity Protection: Enabled
Time since boot: 1 day 8:44
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,4
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16064.0.0,0)
OS Loader Version: 540.120.3~19
Serial Number (system): C02CT0C0PT01
Hardware UUID: C6082A3D-359C-5F2C-AC84-5068C7891897
Provisioning UDID: C6082A3D-359C-5F2C-AC84-5068C7891897
Activation Lock Status: Disabled
Problematic command:
$ python --version
Python 3.8.13
$ gget search -s homo_sapiens 'usf1'
Tue Aug 9 20:03:08 2022 INFO Fetching results from database: homo_sapiens_core_107_38
Tue Aug 9 20:03:11 2022 ERROR The Ensembl server returned the following error: Character set 'utf8' unsupported
Traceback (most recent call last):
File "/Users/areynolds/miniconda3/bin/gget", line 8, in <module>
sys.exit(main())
File "/Users/areynolds/miniconda3/lib/python3.8/site-packages/gget/main.py", line 1223, in main
gget_results = search(
File "/Users/areynolds/miniconda3/lib/python3.8/site-packages/gget/gget_search.py", line 172, in search
df_temp = pd.read_sql(query, con=db_connection)
UnboundLocalError: local variable 'db_connection' referenced before assignment
Using version 0.3.7:
$ gget --version
gget version: 0.3.7
Hi I am running gget version: 0.3.7. When I run alphafold prediction I get this error:
gget alphafold AASEQUENCE
/home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/haiku/_src/data_structures.py:37: FutureWarning: jax.tree_structure is deprecated, and will be removed in a future release. Use jax.tree_util.tree_structure instead.
PyTreeDef = type(jax.tree_structure(None))
Fri Aug 12 20:12:30 2022 INFO Validating input sequence(s).
Using the single-chain model.
Fri Aug 12 20:12:30 2022 INFO Finding closest source for reference database.
Jackhmmer search: 5%|██▉ | 7/147 [elapsed: 11:32 remaining: 3:50:48]
Traceback (most recent call last):
File "/home/ccadmin/anaconda3/envs/gget/bin/gget", line 8, in
sys.exit(main())
File "/home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/gget/main.py", line 1439, in main
alphafold(
File "/home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/gget/gget_alphafold.py", line 467, in alphafold
raw_msa_results = get_msa(
File "/home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/gget/gget_alphafold.py", line 147, in get_msa
raw_msa_results[db_name].extend(jackhmmer_runner.query(fasta_path))
File "/home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/alphafold/data/tools/jackhmmer.py", line 205, in query
os.remove(db_local_chunk(i))
FileNotFoundError: [Errno 2] No such file or directory: '/home/ccadmin/tmp/jackhmmer/fcb45c67-8b27-4156-bbd8-9d11512babf2/uniref90_2021_03.fasta.8'
Any idea how to fix this?
Hello,
Thank you for this awesome tool! I'd love to get ftp links for plant species available in Ensembl Plants. Would this be possible with gget?
Thanks,
Gonzalo
gget will currently create a "tmp" folder in your home directory ("~/tmp/jackhmmer/") for the Jackhmmer search. I think adding an option to change this path is a great idea for a future version. The temporary files will take up to ~2 GB (in case it is possible to free this space until I have implemented your request).
Originally posted by @lauraluebbert in #43 (comment)
Working on a solution.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.