oneLiners.md

Useful one liners

I'm not putting here the one that you can usually find around but rather the ones that I had to make (or had to ask ChatGPT)

Handling fasta files

Make a tsv table from fasta files

First column is sequence id, second is sequence. Can be useful for preparing ENA annotated sequence uploads with many sequences.

for i in $(ls -1 *.fasta); do awk '/^>/ { seq=""; id=substr($0, 2); sub(/[ \t]+$/, "", id); printf("%s\t", id); next } { seq = seq $0 } END { if (seq) print seq }' $i; done > sequence_table.tsv

Handling GTF files

Turn a single space separated GTF (yes, I have seen that on data published with papers)

Will print tabs as spacers between fields 1-8. Spaces in the ninth field are kept. Do note that it inserts an space at the end.

awk 'BEGIN{OFS="\t"} {for (i=1; i<=8; i++) {printf "%s%s", $i, (i==8 ? OFS : OFS)} for (i=9; i<=NF; i++) {printf "%s ", $i} printf "\n"}' input.gtf

If problematic, just remove that last whitespace with: sed 's/ $//g' fix_dmel_scaffold2_merge_V5.gtf > fixed_input.gtf