orfipy
Fast and flexible ORF finder (by urmi-21)
pyfaidx
Efficient pythonic random access to fasta subsequences (by mdshw5)
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| orfipy | pyfaidx | |
|---|---|---|
| 2 | 1 | |
| 46 | 440 | |
| - | - | |
| 1.8 | 6.0 | |
| over 2 years ago | 5 days ago | |
| Python | Python | |
| MIT License | GNU General Public License v3.0 or later |
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.
orfipy
Posts with mentions or reviews of orfipy.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-08-08.
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Looking for a tool to convert a whole fasta file with CDS sequences to a fasta file with protein sequences.
You can probably use or adapt https://github.com/urmi-21/orfipy. I've never used this but it looks fantastic.
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Question about ORF finder
You don't need any specific hardware to run most bioinformatics programs. There is a web application of ORF finder and if you want to run large amounts of analyses you probably want to run them in a Linux environment. Look at Windows Subsystem for Linux if you are a Windows user. You may also be interested in new ORF finders like this one: https://github.com/urmi-21/orfipy
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
What are some alternatives?
When comparing orfipy and pyfaidx you can also consider the following projects:
galaxy - Data intensive science for everyone.
Biopython - Official git repository for Biopython (originally converted from CVS)
biowasm - WebAssembly modules for genomics
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers
reCOGnizer - A tool for domain based annotation with databases from the Conserved Domains Database
FastaParser - A Python FASTA file Parser and Writer.
sublime_text - Issue tracker for Sublime Text
CSIS - Code Safety Inspection Service
biomisc - collection of miscellaneous command line bioinformatic scripts