Output some sections of a text file [closed]

Question

I have input like the following:

>gi|481443199|gb|MH447771.1|
49      0       0       0       1
50      0       0       1       0
>gi|987078004|gb|RTYJ01067061.1|
412     0       0       1       0
413     1       0       0       0
>gi|557075006|gb|ERTJ01078061.1|
41     0       0       1       0
41     1       0       0       0
>gi|787073002|gb|WERJ01045061.1|
612     0       0       1       0
613     1       0       0       0
>gi|887079001|gb|WERJ01045061.1|
715     0       0       1       0
716     1       0       0       0

I want to print some lines, but skip every other line that starts with > (along with all the lines after it, until the subsequent >). For the example input above, the output would be:

>gi|481443199|gb|MH447771.1|
49      0       0       0       1
50      0       0       1       0
>gi|557075006|gb|ERTJ01078061.1|
41     0       0       1       0
41     1       0       0       0
>gi|887079001|gb|WERJ01045061.1|
715     0       0       1       0
716     1       0       0       0

How can I do that?

Answer 1

To skip every other > ... block:

 awk '/^>/ { p = !p } p' input.txt

p is a print flag - p means print when p is true, as the default action is print when none is provided. In awk, variables start out empty, which evaluates to false in Boolean contexts. Every time a > ... line is reached, toggle the p flag.

To print every nth block delimited by > ... lines:

awk -v n=200 '/^>/ { if (skip == 0) skip = n - 1; else --skip; } skip == n - 1' input.txt

It's similar logic, except since n is not 2 we have to use a counter instead of a Boolean flag. Here, skip counts how many more > ... lines to skip before we start printing again. I'm using skip == n - 1 as the print flag as a bit of a short cut.

Answer 2

For awk you can do:

awk 'BEGIN{pr=true}/^>/{pr=!pr}{if (pr) {print}}'

This sets a flag (pr) for when to print, that is toggled every appearance of your token.

Answer 3

$ awk '/^>/{f=f?0:1;}f' file

Just switching a flag variable on and off on encoutering a line beginning with '^'. When it is on, print lines, else don't.

Answer 4

For a more general solution, you can try this:

awk 'k%10==0{print} /^>/ {k++}' input.txt

This increments the variable k every time a line starts with > and prints the lines if k modulo 10 is 0. So, if you want to print every 2nd line, change k%10==0 to k%2==0, for every 200th line change it to k%200==0 etc.

WARNING: In this version, the first line will ALWAYS be printed.