https://github.com/alanwilter/find-pep
https://github.com/alanwilter/find-pep
Last synced: 2 months ago
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- Host: GitHub
- URL: https://github.com/alanwilter/find-pep
- Owner: alanwilter
- Created: 2024-01-17T14:39:42.000Z (over 1 year ago)
- Default Branch: master
- Last Pushed: 2024-06-28T14:52:25.000Z (11 months ago)
- Last Synced: 2025-01-23T13:18:44.029Z (4 months ago)
- Language: Rust
- Size: 20.5 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Fasta tools
## find-pep
```bash
A CLI tool for find peptides in UniProt fasta files
Usage: find-pep
Arguments:
Path to the input FASTA file (required)
Path to the Input peptide list file (required)
Options:
-h, --help Print help
-V, --version Print version
```
- Example
```bash
find-pep input_fasta.fasta input_list.txt | tee output.txt
DTLMISR:F7HL06:1
DTLMISR:A3RFZ7-3:1
DTLMISR:F7F0D6:1
ISRNQVSLTCLVK:F7HL06:1
ISRNQVSLTCLVK:B0FPE9:2
ISRNQVSLTCLVK:F7F0D6:1
```
## fasta-extractor
```bash
Extract FASTA headers from a file.
Usage: fasta-extractor [OPTIONS]
Arguments:
Path to the input FASTA file (required)
Options:
-n, --njobs Number of parallel jobs (default: all available CPUs)
-h, --help Print help
-V, --version Print version
```
- Example
```bash
fasta-extractor input_fasta.fasta | tee output.txt
Extracting headers from FASTA file... using 10 jobs
>tr|F7HL06|F7HL06_MACMU Ig-like domain-containing protein OS=Macaca mulatta OX=9544 PE=4 SV=3
>tr|F7F0D6|F7F0D6_MACMU Ig-like domain-containing protein OS=Macaca mulatta OX=9544 PE=4 SV=3
>sp|Q63ZW7-3|INADL_MOUSE Isoform 3 of InaD-like protein OS=Mus musculus OX=10090 GN=Patj
>sp|B0FPE9|NLRP3_MACMU NACHT, LRR and PYD domains-containing protein 3 OS=Macaca mulatta OX=9544 GN=NLRP3 PE=2 SV=1
>sp|A3RFZ7-3|FCG3A_MACMU Isoform 3 of Low affinity immunoglobulin gamma Fc region receptor III-A OS=Macaca mulatta OX=9544 GN=FCGR3A
```
## Bumping Version
Bump the version number by running `cargo v [part]` where `[part]` is `major`, `minor`, or `patch`, depending on which part of the version number you want to bump.
```bash
cargo install cargo-v
# commit
cargo v patch -y
# push
cargo build --release -j 10
git push origin --tags
```
## Changelog
- 0.2.0
- Added `fasta-extractor`
- 0.1.0
- Initial release with `find-pep`