R-Huerlimann/bioinformatics-one-liners

One line scripts for bioinformatics

One line scripts for bioinformatics

Extracting fasta records

Use samtools faidx

First index the fasta file

samtools faidx mysequences.fasta

Then retrieve sequences by ID

samtools faidx mysequences.fasta id1 id2 id3

Reformatting fasta records

A great tool for this is bioawk .

For example to add a fasta compatible prefix like this

>comp12345_c0_seq1
to
>lcl|comp12345_c0_seq1

can be done with the following bioawk command

bioawk -c fastx '{printf ">lcl|%s\n%s\n", $name, $seq}' original.fasta > reformatted.fasta

Counting the number of sequences in a fasta file

grep -c ">" mysequences.fasta

Untaring multiple files in a folder

for file in *.gz; do tar -xvfz $file;done