[SOLVED] How to do multiple match and print different number of lines after each pattern using awk

Issue

I have a big file with thousand lines that looks like:

>ENST00001234.1
ACGTACGTACGG
TTACCCAGTACG
ATCGCATTCAGC
>ENST00002235.4
TTACGCAT
TAGGCCAG
>ENST00005546.9
TTTATCGC
TTAGGGTAT

I want to grep specific ids (after > sign), for example, ENST00001234.1 then want to get lines after the match until the next > [regardless of the number of lines]. I want to grep about 63 ids in this way at once.

If I grep ENST00001234.1 and ENST00005546.9 ids, the ideal output should be:

>ENST00001234.1
ACGTACGTACGG
TTACCCAGTACG
ATCGCATTCAGC
>ENST00005546.9
TTTATCGC
TTAGGGTAT

I tried awk '/ENST00001234.1/ENST00005546.9/{print}' but it did not help.

Solution

You can set > as the record separator:

$ awk -F'\n' -v RS='>' -v ORS= '$1=="ENST00001234.1"{print RS $0}' ip.txt
>ENST00001234.1
ACGTACGTACGG
TTACCCAGTACG
ATCGCATTCAGC

• -F'\n' to make it easier to compare the search term with first line
• -v RS='>' set > as input record separator
• -v ORS= clear the output record separator, otherwise you'll get extra newline in the output
• $1=="ENST00001234.1" this will do string comparison and matches the entire first line, otherwise you'll have to escape regex metacharacters like . and add anchors
• print RS $0 if match is found, print > and the record content

---

If you want to match more than one search terms, put them in a file:

$ cat f1
ENST00001234.1
ENST00005546.9

$ awk 'BEGIN{FS="\n"; ORS=""}
       NR==FNR{a[$0]; next}
       $1 in a{print RS $0}' f1 RS='>' ip.txt
>ENST00001234.1
ACGTACGTACGG
TTACCCAGTACG
ATCGCATTCAGC
>ENST00005546.9
TTTATCGC
TTAGGGTAT

Here, the contents of f1 is used to build the keys for array a. Once the first file is read, RS='>' will change the record separator for the second file.

$1 in a will check if the first line matches a key in array a

Answered By - Sundeep