PhyloSkims/annotate
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Former-commit-id: bf83f19efe2590803c089697858590aee4720089
Former-commit-id: e7d0bae099d6449b97c431f7ba82568f45bcc005
This commit is contained in:
Eric Coissac
2023-05-11 14:29:43 +02:00
parent 79843c2540
commit 3d9be22e1d
2 changed files with 28 additions and 10 deletions
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1
config/guess_port
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@ -26,6 +26,7 @@ case ${mach}:${syst}:${rels} in
x*86*:Linux:* ) echo i386-linux;; x*86*:Linux:* ) echo i386-linux;;
i*86:Darwin:* ) echo i386-darwin;; i*86:Darwin:* ) echo i386-darwin;;
x*86*:Darwin:* ) echo i386-darwin;; x*86*:Darwin:* ) echo i386-darwin;;
arm64:Darwin:* ) echo arm64-darwin;;
IP*:IRIX*:* ) echo mips-irix;; IP*:IRIX*:* ) echo mips-irix;;
i*86:MINGW32*:* ) echo x86-mingw32;; i*86:MINGW32*:* ) echo x86-mingw32;;

37
summarize_annot.sh
View File

@ -1,12 +1,29 @@
#!/bin/bash #!/bin/bash
egrep "^FT (CDS|rRNA|tRNA) |/gene=" $1 \ resume_ft() {
| awk ' local input=$1
/\/gene=/ && (gene!=1) { grep -E "^FT (CDS|rRNA|tRNA) |/gene=" ${input} \
print $0; | awk '
gene=1 /\/gene=/ && (gene!=1) {
} print $0;
/^FT (CDS|rRNA|tRNA)/ { gene=1
print $0; }
gene=0 /^FT (CDS|rRNA|tRNA)/ {
}' print $0;
gene=0
}'
}
count_tRNA() {
local input=$1
resume_ft $input \
| grep '^FT tRNA' \
| wc -l
}
printf "tRNA genes : %d\n" "$(count_tRNA $1)"