Very simple statistics from fasta files
First, install go,
then:
go install github.com/bjeight/fastats@latest
or
git clone https://github.com/bjeight/fastats.git
cd fastats
go build -o fastats
❯ 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 atgcn_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.p14.genome.fa.bgz | fastats gc | grep "Y"
chrY 0.184749
❯ fastats gc GRCh38.p14.genome.fa.bgz | grep "X"
chrX 0.392343
❯ fastats -h
Very simple statistics from fasta files
Usage:
fastats [command]
Available Commands:
at AT content
atgc ATGC 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
pattern Arbitrary base content
soft Softmasked content
Flags:
-c, --count print counts (default is proportions)
-d, --description write record descriptions (default is IDs)
-f, --file calculate statistics per file (default is per record)
-h, --help help for fastats
-v, --version version for fastats
Use "fastats [command] --help" for more information about a command.
