pyfaidx
Efficient pythonic random access to fasta subsequences (by mdshw5)
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers (by kblin)
| pyfaidx | ncbi-genome-download | |
|---|---|---|
| 1 | 4 | |
| 440 | 890 | |
| - | - | |
| 6.0 | 5.7 | |
| 8 days ago | 9 months ago | |
| Python | Python | |
| GNU General Public License v3.0 or later | Apache License 2.0 |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
pyfaidx
Posts with mentions or reviews of pyfaidx.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-03-07.
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Can anyone recommend notable examples of simple python projects with unit tests?
My package for indexing FASTA files has some extensive tests. Every time someone raised an issue I’d write a test to reproduce the issue and add it after I fix the code. This way I can test for regressions. https://github.com/mdshw5/pyfaidx
ncbi-genome-download
Posts with mentions or reviews of ncbi-genome-download.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-08-02.
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I have a question about the FTP of annotation files from NCBI's Genbank and RefSeq
If you have the taxonomic IDs of your organisms of interest, there are existing parallelized download tools that are more efficient like https://github.com/kblin/ncbi-genome-download or bit-dl-ncbi-assemblies from https://github.com/AstrobioMike/bit
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Bioinformatics without a lab
Downloading from NCBI can be pretty wonky though, but third parties have made good programs to deal with. As an example - and a personal favorite - you have https://github.com/kblin/ncbi-genome-download which by far is the easiest way to download various assembled genomes.
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Downloading genomes from database via command line FTP
I know you said Ensembl, but if you can live with NCBI, I would suggest https://github.com/kblin/ncbi-genome-download
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Downloading viral genomes programmatically
Useful tool to download from NCBI: ncbi-genome-download
What are some alternatives?
When comparing pyfaidx and ncbi-genome-download you can also consider the following projects:
Biopython - Official git repository for Biopython (originally converted from CVS)
galaxy - Data intensive science for everyone.
biowasm - WebAssembly modules for genomics
clinker - Gene cluster comparison figure generator
reCOGnizer - A tool for domain based annotation with databases from the Conserved Domains Database
gisaid-uploader - Simplified & efficient GISAID interactions.
FastaParser - A Python FASTA file Parser and Writer.
OpenWorm - Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
sublime_text - Issue tracker for Sublime Text
CSIS - Code Safety Inspection Service
UPIMAPI - UniProt Id Mapping through API
pyfaidx vs Biopython
ncbi-genome-download vs galaxy
pyfaidx vs biowasm
ncbi-genome-download vs clinker
pyfaidx vs reCOGnizer
ncbi-genome-download vs gisaid-uploader
pyfaidx vs FastaParser
ncbi-genome-download vs OpenWorm
pyfaidx vs sublime_text
ncbi-genome-download vs Biopython
pyfaidx vs CSIS
ncbi-genome-download vs UPIMAPI