User:Timothee Flutre/Notebook/Postdoc/2012/05/25

One-liners with GNU tools

• Tutorial: Introduction to text manipulation on UNIX-based systems by Brad Yoes (IBM)

• Toolbox:
  • AWK
  • grep
  • sed
  • cut
  • tr
  • wc

• Skip a subset of successive lines:

for i in {1..10}; do echo $i; done | sed 3,6d

• Extract a subset of successive lines:

for i in {1..20}; do echo $i; done | sed -n 3,5p

• Use absolute values:

for i in {-5..5}; do echo $i; done | awk 'function abs(x){return (((x < 0.0) ? -x : x) + 0.0)} {print abs($1)}'

• Convert file from fasta to fastq: we can use the built-in variable "RS" (split records) and use "split" (string function):

awk 'BEGIN{RS=">"} {if(NF==0)next; split($0,a,"\n"); printf "@"a[1]"\n"a[2]"\n+\n"; \
for(i=1;i<=length(a[2]);i++)printf "}"; printf"\n"}' probes.fa > probes.fq