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https://github.com/kullrich/korthocpp
korthoCPP calculates pairwise kmer jaccard distance between two peptide fasta files
https://github.com/kullrich/korthocpp
Last synced: 4 days ago
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korthoCPP calculates pairwise kmer jaccard distance between two peptide fasta files
- Host: GitHub
- URL: https://github.com/kullrich/korthocpp
- Owner: kullrich
- License: mit
- Created: 2024-03-04T21:35:45.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2024-03-05T07:35:48.000Z (8 months ago)
- Last Synced: 2024-03-05T23:49:32.638Z (8 months ago)
- Language: C++
- Size: 601 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# korthoCPP 
korthoCPP calculates pairwise kmer jaccard distance between two peptide fasta files
## Download and compile
```
git clone https://github.com/kullrich/korthoCPP.git
cd korthoCPP && make clean && make
```
## Usage
```
Usage: korthoCPP [options] -q -t
Options:
-q FILE query peptide fasta file
-t FILE target peptide fasta file
-o FILE output file to write jaccard distances
-k INT kmer length [default: 6]
-m DOUBLE min jaccard distance to report pair [default: 0.01]
-s DOUBLE sparse threshold to switch search strategy [defualt: 0.1]
-n INT number of kmers to check for sparse [default: 20]
-p INT number of threads [default: 1]
-d debug
```
## Compare two peptide fasta files and calcualte jaccard distances
```
korthoCPP -q query.fasta -t target.fasta
```
### use multiple threads
```
korthoCPP -q query.fasta -t target.fasta -p 2
```
### use different min jaccard
```
korthoCPP -q query.fasta -t target.fasta -m 0.02
```
## Example
```
wget https://www.pseudomonas.com/downloads/pseudomonas/pgd_r_22_1/Pseudomonas_aeruginosa_PAO1_107/Pseudomonas_aeruginosa_PAO1_107.faa.gz
wget https://www.pseudomonas.com/downloads/pseudomonas/pgd_r_22_1/Pseudomonas_fluorescens_SBW25_116/Pseudomonas_fluorescens_SBW25_116.faa.gz
gunzip Pseudomonas_aeruginosa_PAO1_107.faa.gz
gunzip Pseudomonas_fluorescens_SBW25_116.faa.gz
./korthoCPP -q Pseudomonas_aeruginosa_PAO1_107.faa -t Pseudomonas_fluorescens_SBW25_116.faa -p 4 -d
```
```
Time taken: kmer extraction 7059 milliseconds
number of sequences Q: 5586
number of sequences T: 5861
Time taken: QkmerMap creation 7091 milliseconds
number of kmers QkmerMap: 1612859
Time taken: TkmerMap creation 8469 milliseconds
number of kmers TkmerMap: 1734068
number of sparse candidate pairs: 345
sparse value: 1.05377e-05 < sparse threshold: 0.1 >>> search strategy one vs one
Time taken: check sparse threshold 1 milliseconds
Time taken: candidate pairs creation 1423 milliseconds
number of candidate pairs: 409274
Time taken: distance calculation 44714 milliseconds
```
```
head output.txt
###
qname tname jaccard mash ani sumdist
PA0034 PFLU1157 0.0303797 0.471793 0.528207 0.941032
PA0032 PFLU0028 0.087344 0.304749 0.695251 0.839344
PA0029 PFLU0025 0.057554 0.369641 0.630359 0.891156
PA0030 PFLU0026 0.0470383 0.401602 0.598398 0.91015
PA0031 PFLU0027 0.215854 0.172576 0.827424 0.644935
PA0035 PFLU0035 0.272947 0.141111 0.858889 0.571157
PA0036 PFLU0036 0.473297 0.0737314 0.926269 0.3575
PA0037 PFLU0037 0.110476 0.269099 0.730901 0.801029
PA0038 PFLU0039 0.147826 0.226074 0.773926 0.742424
```