gfastats

Let's get some test files first:

mv gfastar/docs/testFiles-gfastats/* .

Help:

gfastats -h

File:

cat random1.fasta

Summary statistics:

gfastats random1.fasta

Tabular output:

gfastats random1.fasta -t

Change locale:

gfastats large_input.fasta.gz --locale en_US.UTF-8

Full output:

gfastats random1.fasta --nstar-report

Report by sequence:

gfastats random1.fasta --seq-report

Original file:

gfastats random1.fasta -ofa

Line length:

gfastats random1.fasta -ofa --line-length 2

Subset:

gfastats random1.fasta Header2 -ofa

Subset with bed:

gfastats random1.fasta -e <(echo Header2) -ofa

cat random1.fasta.bed`

gfastats random1.fasta -ofa -e random1.fasta.bed

gfastats random1.fasta -ofa -i random1.fasta.bed

Size of components:

gfastats random1.fasta -s s

gfastats random1.fasta -s c

gfastats random1.fasta -s g

AGP:

gfastats random1.fasta -b a

BED coordinates:

gfastats random1.fasta -b s

gfastats random1.fasta -b c

gfastats random1.fasta -b g

Sorting:

gfastats random1.fasta -ofa --sort largest

gfastats random1.fasta -ofa --sort descending

gfastats random1.fasta -ofa --sort random1.sort

GFA2:

gfastats random1.gfa2 -o gfa2

GFA2 to FASTA conversion:

gfastats random1.gfa2 -o fasta

GFA2 to GFA1 conversion:

gfastats random1.gfa2 -o gfa

GFA1:

gfastats random2.gfa -o gfa

GFA1 to FASTA:

gfastats random2.gfa -o fasta

GFA1 to GFA2:

gfastats random2.gfa -o gfa2

GFA1 no sequence:

gfastats random2.noseq.gfa -o gfa

GFA1 no sequence:

gfastats random2.noseq.gfa -o fa

Homopolymer compression:

gfastats random1.fasta --homopolymer-compress 1 -ofa

Find terminal overlaps:

gfastats random5.findovl.gfa -ogfa

gfastats random5.findovl.gfa --discover-terminal-overlaps 3 -ogfa

Discover paths:

gfastats random1.fasta -ogfa | grep -v "^P" > test.gfa

gfastats test.gfa -ogfa

gfastats test.gfa -ogfa2 --discover-paths

Superimpose AGP:

gfastats random1.fasta -a random1.agp -ofa

SAK reverse complement:

cat random1.rvcp.sak

gfastats random1.fasta -ofa

gfastats random1.fasta -k random1.rvcp.sak -ofa

Other SAK instructions:

cat random1.instructions.sak
gfastats random1.fasta -ofa
gfastats random1.fasta -ofa -k <(head -1 random1.instructions.sak)
gfastats random1.fasta -ofa -k <(head -2 random1.instructions.sak)
gfastats random1.fasta -ofa -k <(head -3 random1.instructions.sak)
gfastats random1.fasta -ofa -k <(head -4 random1.instructions.sak)
gfastats random1.fasta -ogfa2 -k <(head -4 random1.instructions.sak)
gfastats random1.fasta -ofa -k <(head -5 random1.instructions.sak)
gfastats random1.fasta -ogfa2 -k <(head -5 random1.instructions.sak)
gfastats random1.fasta -ofa -k <(head -6 random1.instructions.sak)
gfastats random1.fasta -ogfa2 -k <(head -6 random1.instructions.sak)
gfastats random1.fasta -ogfa2 -k <(head -6 random1.instructions.sak)
gfastats random1.fasta -ogfa2 -k <(head -7 random1.instructions.sak)
gfastats random1.fasta -ofa -k <(head -8 random1.instructions.sak)