Command for counting gene model after each round of MAKER

Question

[Elizabeth]

Hello, I am looking for a command that can tell me the number of gene models after each round of MAKER. I have tried the following:

less Maker2.all.gff |awk '$3=="mRNA"' |grep "mRNA-1" |awk '{print $5-$4}' |summary.sh

cat <roundN.full.gff> | awk '{ if ($3 == "gene") print $0 }' | awk '{ sum += ($5 - $4) } END { print NR, sum / NR }'

But, my terminal seems to hang, every time I run the command. Has anyone encountered a similar problem ?

[Juke34]

What does summary.sh ?

Answer 1

[ringourquia]

The "fathom -gene-stats" command used in the path to generate the SNAP learning-file displays several stats of your gff including the number of genes. Otherwise, I use:

cut -f3 your_merged_gff.gff | grep "gene" | wc -l

[Elizabeth]

Thank you. It works.