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Bioawk

Bioawk is an awk extension for biological formats written by Dr. Heng Li.
See the documentation here .

Install on MacOS with the Homebrew package manager

$ brew install bioawk

Conda

conda install -c bioconda bioawk

Install from source

$ git clone git://github.com/lh3/bioawk.git
$ cd bioawk && make 

# Make sure that bioawk is in your $PATH or use the full path to call the executable.

🗒 Several tutorial on the net suggest installing it with sudo in you system path - no need for that. This is another way to say - avoid unnecessary (it is bad practice) installation of tools as root. You will not be able to do it on any computer center anyway. 🔐

If you get error about 

...
make: yacc: Command not found

then you need install few packages (root privileges required)

$ sudo apt-get install bison byacc

Examples

bioawk supported formats

$ bioawk -c help

bed:
    1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart 8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts 
sam:
    1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext 9:tlen 10:seq 11:qual 
vcf:
    1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info 
gff:
    1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter 8:strand 9:group 10:attribute 
fastx:
    1:name 2:seq 3:qual 4:comment

We will use GTF and FASTA files for the chr17:7400001-7800000 region, downloaded using the UCSC Table Browser.

  • chr17_fragm.gtf
  • chr17_fragm.fasta

use the file chr17_fragm.gtf

$ bioawk -c gff  '$3 ~ /exon/ {print $seqname, $feature, $end-$start}' chr17_fragm.gtf | sort -nk3

use the file chr17_fragm.fasta

Count the number of FASTA entries

$ bioawk -c fastx 'END{print NR}' chr17_fragm.fasta

Reverse complement the sequences

$ bioawk -c fastx '{print ">"$name"\n"revcomp($seq)}' chr17_fragm.fasta > chr17_fragm.revcomp.fasta | head -n 2

$ head -n 2 chr17_fragm.fasta
$ head -n 2 chr17_fragm.revcomp.fasta

Create a table with the sequence length in the FASTA file.

$ bioawk -c fastx '{print $name,length($seq)}' chr17_fragm.fasta > chr17_fragm.fasta.seqlen | head -n 10 chr17_fragm.fasta.seqlen
$ head -n 10 chr17_fragm.fasta.seqlen