awk NR==FNR for command syntax

Question

I am having trouble using awk NR==FNR to return lines of interest from an input .fastq file.

I have the following example input file called example.fastq

@SRR1111111.1 1/1
CTGGANAAGTGAAATAATATAAATTTTTCCACTATTGAATAAAAGCAACTTAAATTTTCTAAGTCG
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEA<AAEEEEE<6
@SRR1111111.2 2/1
CTATANTATTCTATATTTATTCTAGATAAAAGCATTCTATATTTAGCATATGTCTAGCAAAAAAAA
+
AAAAA#EE6EEEEEEEEEEEEAAEEAEEEEEEEEEEEE/EAE/EAE/EA/EAEAAAE//EEAEAA6
@SRR1111111.3 3/1
CTATANTATTGAAATAATAATGTAGATAAAACTATTGAATAACAGCAACTTAAATTTTCAATAAGA
+
AAAAA#EE6EEEEEEEEEEEEAAEEAEEEEEEEEEEEE/EAE/EAE/EA/EAEAAAE//EEAEAA6

I am trying to extract groups of four lines that contain a string of interest, importantly approximate matches must be allowed hence the use of agrep instead of grep. The below example works.

agrep -1 -n "GAAATAATA" example.fastq | awk -F: 'NR==FNR{for(i=($1-1);i<=($1+2);i++)a[i];next}FNR in a' - example.fastq

The above command produces the following correct output.

@SRR1111111.1 1/1
CTGGANAAGTGAAATAATATAAATTTTTCCACTATTGAATAAAAGCAACTTAAATTTTCTAAGTCG
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEA<AAEEEEE<6
@SRR1111111.3 3/1
CTATANTATTGAAATAATAATGTAGATAAAACTATTGAATAACAGCAACTTAAATTTTCAATAAGA
+
AAAAA#EE6EEEEEEEEEEEEAAEEAEEEEEEEEEEEE/EAE/EAE/EA/EAEAAAE//EEAEAA6

However if I use a sequence not contained in the second line this command still prints the top two lines as in the following example.

agrep -1 -n "TAGATAAAACT" example.fastq | awk -F: 'NR==FNR{for(i=($1-1);i<=($1+2);i++)a[i];next}FNR in a' - example.fastq

@SRR1111111.1 1/1
CTGGANAAGTGAAATAATATAAATTTTTCCACTATTGAATAAAAGCAACTTAAATTTTCTAAGTCG
@SRR1111111.3 3/1
CTATANTATTGAAATAATAATGTAGATAAAACTATTGAATAACAGCAACTTAAATTTTCAATAAGA
+
AAAAA#EE6EEEEEEEEEEEEAAEEAEEEEEEEEEEEE/EAE/EAE/EA/EAEAAAE//EEAEAA6

Thanks for helping me understand the behavior of this awk command.

Answer 1

You may use this agrep + awk solution:

srch() {
   awk -F ': ' 'NR==FNR {
      a[$1] = 1
      next
   }
   a[FNR] {
      print p
      print
      for (i=0; i<2 && getline > 0; i++)
         print
   }
   {
      p=$0
   }' <(agrep -1 -n "$2" "$1") "$1"
}

Then run it as:

srch file 'GAAATAATA'

@SRR1111111.1 1/1
CTGGANAAGTGAAATAATATAAATTTTTCCACTATTGAATAAAAGCAACTTAAATTTTCTAAGTCG
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEA<AAEEEEE<6
@SRR1111111.3 3/1
CTATANTATTGAAATAATAATGTAGATAAAACTATTGAATAACAGCAACTTAAATTTTCAATAAGA
+
AAAAA#EE6EEEEEEEEEEEEAAEEAEEEEEEEEEEEE/EAE/EAE/EA/EAEAAAE//EEAEAA6

and this:

srch file 'TAGATAAAACT

@SRR1111111.3 3/1
CTATANTATTGAAATAATAATGTAGATAAAACTATTGAATAACAGCAACTTAAATTTTCAATAAGA
+
AAAAA#EE6EEEEEEEEEEEEAAEEAEEEEEEEEEEEE/EAE/EAE/EA/EAEAAAE//EEAEAA6'