pyfaidx
Efficient pythonic random access to fasta subsequences (by mdshw5)
biomisc
collection of miscellaneous command line bioinformatic scripts (by olgatsiouri1996)
| pyfaidx | biomisc | |
|---|---|---|
| 1 | 2 | |
| 440 | 7 | |
| - | - | |
| 6.0 | 4.5 | |
| 8 days ago | 5 months ago | |
| Python | Python | |
| GNU General Public License v3.0 or later | MIT License |
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
biomisc
Posts with mentions or reviews of biomisc.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-04-06.
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Biopython quarry on protein sequencing
if you know witch exactly residues do you want to retrieve from your pdb you can use this: subset_pdb_to_fasta.py
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Extract sequences given FASTA + list of starts and ends?
i have made one with python: trim_fasta_by_coords.py. I have a newer version that deals with strands but since you work with proteins you don't need it
What are some alternatives?
When comparing pyfaidx and biomisc you can also consider the following projects:
Biopython - Official git repository for Biopython (originally converted from CVS)
DnaChisel - :pencil2: A versatile DNA sequence optimizer
biowasm - WebAssembly modules for genomics
PDBaser - Protein preparation for MD, made faster and easier !
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers
pycm - Multi-class confusion matrix library in Python
reCOGnizer - A tool for domain based annotation with databases from the Conserved Domains Database
readfq - Fast multi-line FASTA/Q reader in several programming languages
FastaParser - A Python FASTA file Parser and Writer.
sublime_text - Issue tracker for Sublime Text
CSIS - Code Safety Inspection Service