hi there internet, you found my repository. I am just putting stuff here to store scripts for publications and share with labmates.
| function | code |
|---|---|
| Replace fasta headers with FILENAME_ENTRY | awk '/^>/ {gsub(/.fa(sta)?$/,"",FILENAME);printf(">%s\n",++i "_" FILENAME);next;} {print}' input.fa |
| Remove redundant entries from a multifasta file. | awk '/^>/{f=!d[$1];d[$1]=1}f' singleline.fasta > singleline.unique.fasta |
| Convert multiline fasta to single line. | awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < multi.fasta | tail -n+2 > single.fasta |
| select all entries from a gtdbtk MSA file that match a pattern | grep -A 1 "p__Myxo" --no-group-separator gtdbtk.bac120.msa.fasta > bins.txt |
| remove prodigal metadata from faa header | sed 's/\ .*$//' input.faa > input_red.faa |
| convert single line fasta to tsv file | awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input.single.fasta > input.tsv |