GREP或AWK：搜索每行的前N个字符，并输出与模式匹配的周围的行

Question

I have a RNA-seq data that looks like this:

@J00157:85:HNNJLBBXX:5:1101:2869:15047 1:N:0:ATTACTCG+TATAGCCT
CGACGCTCTTCCGATCTGAGCTGCAGCCTCGGCCCCAGGATCCCCCTGGGGGACTGGACGCTGCTATTGATTCACGAGGCGCTCAGATCGGAAGAGCACAC
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJFJJJJJJFJJJJJJJJFJJJFJFJJJJJJJJJJJJJJJJ
--
@J00157:85:HNNJLBBXX:5:1101:12550:15574 1:N:0:ATTACTCG+TATAGCCT
GCTCTTCCGATCTGCTATTGATGACTGTCCTCTGTTCTTTCTTTCACAGTAGACGAGGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTACTC
+
AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
--

If we treat all content after @ as a section, you can see only the second line is the real sequencing information, 1,3,4,5 are logistic/quality information.

The goal is to extract sequences (second line information) that containing "GCTGCA" in the first N (N=35) characters each line , and at the same time output the surrounding lines (1 line ahead, 3 line behind the matched line) .

An example answer is

@J00157:85:HNNJLBBXX:5:1101:2869:15047 1:N:0:ATTACTCG+TATAGCCT
CGACGCTCTTCCGATCTGAGCTGCAGCCTCGGCCCCAGGATCCCCCTGGGGGACTGGACGCTGCTATTGATTCACGAGGCGCTCAGATCGGAAGAGCACAC
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJFJJJJJJFJJJJJJJJFJJJFJFJJJJJJJJJJJJJJJJ
--

What I have tried are

awk 'substr($0, 1, 35) ~ "GCTGCA"' filename.fastq > newfile.fastq
grep -B 1 -A 2 -E GCTGCA filename.fastq > newfile.fastq
awk '{a[++i]=$0;}{substr(a[++i], 1, 35) ~ "GCTGCA"}{for(j=NR-1;j<=NR+2;j++)print a[j];}' filename.fastq > newfile.fastq

The first one cannot output surrounding lines. The second one cannot limit pattern-matching in the first 35 letters of each line. The third line should work, but it gives me wired output (which obviously is not correct):

@J00157:85:HNNJLBBXX:5:1101:14235:1367 1:N:0:ATTACTCG+TATAGCCT
@J00157:85:HNNJLBBXX:5:1101:14235:1367 1:N:0:ATTACTCG+TATAGCCT
TCTNCTCTTCCGATCTACCCCACACACCCCCGCCGCCGCCGCCGCCGCCGCCCTCCGACGCACACCACACGCGCGCGCGCGCGCGCCGCCCCCGCCGCTCC
TCTNCTCTTCCGATCTACCCCACACACCCCCGCCGCCGCCGCCGCCGCCGCCCTCCGACGCACACCACACGCGCGCGCGCGCGCGCCGCCCCCGCCGCTCC
+
+
AAF#FJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFJJAJJJJJFJJJJ7JJ
AAF#FJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFJJAJJJJJFJJJJ7JJ
--
--

Answer 1

with gawk multi-char RS support.

awk -v RS='\n--' -F'\n' 'substr($2,0,35)~"GCTGCA"{print $0 RS}' file

you define the record with the record separator.

Answer 2

With awk using getline :

search.awk :

substr($0,0,35)~"GCTGCA"  {
    print p # Print the previous line ...
    print # ... , current line ...
    for(i=0;i<=2;i++) { # ... and the 3 lines following it
        getline
        print
    }
}

# Store the previous line
{ p = $0 }

Call it like this:

awk -f search.awk input_file

---

Or without regular expressions and with a parameter:

search.awk

index(substr($0,0,35), search)  {
    print l
    print
    for(i=0;i<=2;i++) {
        getline
        print
    }
}

{ l = $0 }

Call it like

awk -v search="GCTGCA" -f search.awk input_file