https://github.com/bjeight/fastats
Very simple statistics from fasta files
https://github.com/bjeight/fastats
bioinformatics fasta genomics
Last synced: 3 months ago
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Very simple statistics from fasta files
- Host: GitHub
- URL: https://github.com/bjeight/fastats
- Owner: bjeight
- Created: 2023-08-16T21:27:59.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-11-13T13:45:15.000Z (7 months ago)
- Last Synced: 2025-11-13T15:26:44.877Z (7 months ago)
- Topics: bioinformatics, fasta, genomics
- Language: Go
- Homepage:
- Size: 94.7 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# fastats
Very simple statistics from fasta files
### Installation
First, [install go](https://go.dev/dl/),
then:
```
go install github.com/bjeight/fastats@latest
```
or
```
git clone https://github.com/bjeight/fastats.git
cd fastats
go build -o fastats
```
### Example usage
```
❯ fastats at PlasmoDB-64_Pfalciparum3D7_Genome.fasta
record ATat_prop
Pf3D7_01_v3 0.794985
Pf3D7_02_v3 0.802509
Pf3D7_03_v3 0.799358
Pf3D7_04_v3 0.794851
Pf3D7_05_v3 0.806723
Pf3D7_06_v3 0.802128
Pf3D7_07_v3 0.801507
Pf3D7_08_v3 0.804305
Pf3D7_09_v3 0.809843
Pf3D7_10_v3 0.803563
Pf3D7_11_v3 0.810128
Pf3D7_12_v3 0.806968
Pf3D7_13_v3 0.810485
Pf3D7_14_v3 0.815636
Pf3D7_API_v3 0.857839
Pf3D7_MIT_v3 0.684096
```
```
❯ fastats soft -f *softmasked.fasta
file soft_prop
Pad.softmasked.fasta 0.612057
Pbi.softmasked.fasta 0.545409
Pbl.softmasked.fasta 0.576649
Pfa.softmasked.fasta 0.519676
Pga.softmasked.fasta 0.610234
Ppr.softmasked.fasta 0.539591
Pre.softmasked.fasta 0.535700
```
```
❯ bgzip -d -c GRCh38.primary_assembly.genome.fa.bgz | fastats gc | grep "Y"
chrY 0.184749
```
```
❯ fastats gc GRCh38.primary_assembly.genome.fa.bgz | grep "X"
chrX 0.392343
```
```
❯ fastats assembly GRCh38.primary_assembly.genome.fa
file n_records length N50 N90 L50 L90
GRCh38.primary_assembly.genome.fa 194 3099750718 145138636 80373285 9 19
```
### Help
```
❯ fastats -h
Very simple statistics from fasta files
Usage:
fastats {command} [flags]
fastats [command]
Available Commands:
ambig Ambiguous content
assembly Assembly statistics
at AT content
atgc ATGC content
content Arbitrary base content
gaps Gap content
gc GC content
help Help about any command
len Sequence length
n N content
names Record names
num Number of records
soft Softmasked content
Flags:
-h, --help help for fastats
-l, --licences print licence information and exit
-v, --version version for fastats
Use "fastats [command] --help" for more information about a command.
```