gget

🧬 gget enables efficient querying of genomic reference databases

Science Score: 67.0%

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Keywords

alphafold alphafold2 archs4 blast databases enrichment-analysis enrichr ensembl genomics gget ncbi proteomics reference rna-seq transcriptomics uniprot

Last synced: 4 months ago · JSON representation ·

Repository

🧬 gget enables efficient querying of genomic reference databases

Basic Info

Host: GitHub
Owner: pachterlab
License: bsd-2-clause
Language: Python
Default Branch: main
Homepage: https://gget.bio
Size: 330 MB

Statistics

Stars: 1,049
Watchers: 8
Forks: 77
Open Issues: 20
Releases: 36

Topics

alphafold alphafold2 archs4 blast databases enrichment-analysis enrichr ensembl genomics gget ncbi proteomics reference rna-seq transcriptomics uniprot

Created over 3 years ago · Last pushed 5 months ago

Metadata Files

Readme Contributing License Code of conduct Citation

gget

gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.

alt text

If you use gget in a publication, please cite*:
Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836 Read the article here: https://doi.org/10.1093/bioinformatics/btac836

Installation

bash uv pip install gget or bash pip install --upgrade gget

For use in Jupyter Lab / Google Colab: ```python

Python

import gget ```

🔗 Manual

🪄 Quick start guide

Command line: ```bash

Fetch all Homo sapiens reference and annotation FTPs from the latest Ensembl release

$ gget ref homo_sapiens

Get Ensembl IDs of human genes with "ace2" or "angiotensin converting enzyme 2" in their name/description

$ gget search -s homo_sapiens 'ace2' 'angiotensin converting enzyme 2'

Look up gene ENSG00000130234 (ACE2) and its transcript ENST00000252519

$ gget info ENSG00000130234 ENST00000252519

Fetch the amino acid sequence of the canonical transcript of gene ENSG00000130234

$ gget seq --translate ENSG00000130234

Quickly find the genomic location of (the start of) that amino acid sequence

$ gget blat MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS

BLAST (the start of) that amino acid sequence

$ gget blast MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS

Align multiple nucleotide or amino acid sequences against each other (also accepts path to FASTA file)

$ gget muscle MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS MSSSSWLLLSLVEVTAAQSTIEQQAKTFLDKFHEAEDLFYQSLLAS

Align one or more amino acid sequences against a reference (containing one or more sequences) (local BLAST) (also accepts paths to FASTA files)

$ gget diamond MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS -ref MSSSSWLLLSLVEVTAAQSTIEQQAKTFLDKFHEAEDLFYQSLLAS

Use Enrichr for an ontology analysis of a list of genes

$ gget enrichr -db ontology ACE2 AGT AGTR1 ACE AGTRAP AGTR2 ACE3P

Get the human tissue expression of gene ACE2

$ gget archs4 -w tissue ACE2

Get the protein structure (in PDB format) of ACE2 as stored in the Protein Data Bank (PDB ID returned by gget info)

$ gget pdb 1R42 -o 1R42.pdb

Find Eukaryotic Linear Motifs (ELMs) in a protein sequence

$ gget setup elm # setup only needs to be run once $ gget elm -o results MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS

Fetch a scRNAseq count matrix (AnnData format) based on specified gene(s), tissue(s), and cell type(s) (default species: human)

$ gget setup cellxgene # setup only needs to be run once $ gget cellxgene --gene ACE2 SLC5A1 --tissue lung --celltype 'mucus secreting cell' -o exampleadata.h5ad

Predict the protein structure of GFP from its amino acid sequence

$ gget setup alphafold # setup only needs to be run once $ gget alphafold MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK Python (Jupyter Lab / Google Colab):python
import gget gget.ref("homosapiens") gget.search(["ace2", "angiotensin converting enzyme 2"], "homosapiens") gget.info(["ENSG00000130234", "ENST00000252519"]) gget.seq("ENSG00000130234", translate=True) gget.blat("MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS") gget.blast("MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS") gget.muscle(["MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS", "MSSSSWLLLSLVEVTAAQSTIEQQAKTFLDKFHEAEDLFYQSLLAS"]) gget.diamond("MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS", reference="MSSSSWLLLSLVEVTAAQSTIEQQAKTFLDKFHEAEDLFYQSLLAS") gget.enrichr(["ACE2", "AGT", "AGTR1", "ACE", "AGTRAP", "AGTR2", "ACE3P"], database="ontology", plot=True) gget.archs4("ACE2", which="tissue") gget.pdb("1R42", save=True)

gget.setup("elm") # setup only needs to be run once orthodf, regexdf = gget.elm("MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS")

gget.setup("cellxgene") # setup only needs to be run once gget.cellxgene(gene = ["ACE2", "SLC5A1"], tissue = "lung", cell_type = "mucus secreting cell")

gget.setup("alphafold") # setup only needs to be run once gget.alphafold("MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK") Call `gget` from R using [reticulate](https://rstudio.github.io/reticulate/):r system("pip install gget") install.packages("reticulate") library(reticulate) gget <- import("gget")

gget$ref("homosapiens") gget$search(list("ace2", "angiotensin converting enzyme 2"), "homosapiens") gget$info(list("ENSG00000130234", "ENST00000252519")) gget$seq("ENSG00000130234", translate=TRUE) gget$blat("MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS") gget$blast("MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS") gget$muscle(list("MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS", "MSSSSWLLLSLVEVTAAQSTIEQQAKTFLDKFHEAEDLFYQSLLAS"), out="out.afa") gget$diamond("MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLAS", reference="MSSSSWLLLSLVEVTAAQSTIEQQAKTFLDKFHEAEDLFYQSLLAS") gget$enrichr(list("ACE2", "AGT", "AGTR1", "ACE", "AGTRAP", "AGTR2", "ACE3P"), database="ontology") gget$archs4("ACE2", which="tissue") gget$pdb("1R42", save=TRUE) ```

Owner

Name: Pachter Lab
Login: pachterlab
Kind: organization
Email: lpachter@caltech.edu
Location: Pasadena, CA

Website: http://pachterlab.github.io
Repositories: 128
Profile: https://github.com/pachterlab

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use gget in a publication, please cite it as below."
authors:
- family-names: "Luebbert"
  given-names: "Laura"
  orcid: "https://orcid.org/0000-0003-1379-2927"
- family-names: "Pachter"
  given-names: "Lior"
  orcid: "https://orcid.org/0000-0002-9164-6231"
title: "gget"
# version: 0.2.6
doi: "10.1093/bioinformatics/btac836"
# date-released: 2022
url: "https://github.com/pachterlab/gget"
preferred-citation:
  type: article
  authors:
  - family-names: "Luebbert"
    given-names: "Laura"
    orcid: "https://orcid.org/0000-0003-1379-2927"
  - family-names: "Pachter"
    given-names: "Lior"
    orcid: "https://orcid.org/0000-0002-9164-6231"
  doi: "10.1093/bioinformatics/btac836"
  journal: "Bioinformatics"
#   month: 9
#   start: 1 # First page number
#   end: 10 # Last page number
  title: "Efficient querying of genomic reference databases with gget"
#   issue: 1
#   volume: 1
  year: 2023

GitHub Events

Total

Create event: 4
Release event: 2
Issues event: 15
Watch event: 113
Delete event: 1
Member event: 2
Issue comment event: 25
Push event: 297
Pull request event: 13
Fork event: 7

Last Year

Create event: 4
Release event: 2
Issues event: 15
Watch event: 113
Delete event: 1
Member event: 2
Issue comment event: 25
Push event: 297
Pull request event: 13
Fork event: 7

Committers

Last synced: 8 months ago

All Time

Total Commits: 2,810
Total Committers: 18
Avg Commits per committer: 156.111
Development Distribution Score (DDS): 0.212

Past Year

Commits: 593
Committers: 7
Avg Commits per committer: 84.714
Development Distribution Score (DDS): 0.266

Top Committers

Name	Email	Commits
Laura Luebbert	5****t	2,213
choang	c**g@c**u	397
techno-sam	7****m	82
josephrich98	j**8@g**m	72
Chi Hoang	3****2	12
Victor Garcia Ruiz	5****5	9
vecerkovakaterina	v**1@g**m	6
Gavin John	g**n@g**m	4
Lior Pachter	l**r@g**m	3
noriakis	3****s	3
DylanLawless	d**s@e**h	2
Arman	3****n	1
Austin	a**1@g**m	1
Christian Brueffer	c**n@b**o	1
JJ	1****s	1
Nils Homer	n****3	1
Tomás Di Domenico	t**o@t**u	1
Mayuko Boffelli	m**i@u**u	1

Committer Domains (Top 20 + Academic)

ucla.edu: 1 tdido.eu: 1 brueffer.io: 1 epfl.ch: 1 caltech.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 75
Total pull requests: 99
Average time to close issues: 2 months
Average time to close pull requests: 8 days
Total issue authors: 52
Total pull request authors: 17
Average comments per issue: 2.53
Average comments per pull request: 0.32
Merged pull requests: 93
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 12
Pull requests: 16
Average time to close issues: about 2 months
Average time to close pull requests: 21 days
Issue authors: 7
Pull request authors: 6
Average comments per issue: 1.58
Average comments per pull request: 0.63
Merged pull requests: 13
Bot issues: 0
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Pull Request Authors

lauraluebbert (64)
techno-sam (23)
anhchi172 (12)
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Issue Labels

enhancement (36) bug (1)

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Packages

Total packages: 2
Total downloads:
- pypi 30,656 last-month
Total docker downloads: 58

Total dependent packages: 4
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Total dependent repositories: 3
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Total versions: 100
Total maintainers: 1

pypi.org: gget

Efficient querying of genomic databases.

Homepage: https://github.com/pachterlab/gget
Documentation: https://gget.readthedocs.io/
License: BSD-2
Latest release: 0.29.2
published 6 months ago

Versions: 54
Dependent Packages: 4
Dependent Repositories: 3
Downloads: 30,656 Last month
Docker Downloads: 58

Rankings

Stargazers count: 2.2%

Dependent packages count: 3.2%

Docker downloads count: 3.3%

Average: 5.0%

Forks count: 5.6%

Downloads: 6.8%

Dependent repos count: 9.0%

Maintainers (1)

lauraluebbert

Last synced: 5 months ago

proxy.golang.org: github.com/pachterlab/gget

Documentation: https://pkg.go.dev/github.com/pachterlab/gget#section-documentation
License: bsd-2-clause
Latest release: v0.29.2
published 6 months ago

Versions: 46
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 5 months ago

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dev-requirements.txt pypi

coverage >=5.1 development
lxml * development
pytest >=7.0.0 development

requirements.txt pypi

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setup.py pypi