Counting specific lines that don't contain specific word

Question

Please I have question: I have a file like this

@HWI-ST273:296:C0EFRACXX:2:2101:17125:145325/1
TTAATACACCCAACCAGAAGTTAGCTCCTTCACTTTCAGCTAAATAAAAG
+
8?8A;DDDD;@?++8A?;C;F92+2A@19:1*1?DDDECDE?B4:BDEEI
@BBBB-ST273:296:C0EFRACXX:2:1303:5281:183410/1
TAGCTCCTTCGCTTTCAGCTAAATAAAAGCCCAGTACTTCTTTTTTACCA
+
CCBFFFFFFHHHHJJJJJJJJJIIJJJJJJJJJJJJJJJJJJJIJJJJJI
@HWI-ST273:296:C0EFRACXX:2:1103:16617:140195/1
AAGTTAGCTCCTTCGCTTTCAGCTAAATAAAAGCCCAGTACTTCTTTTTT
+
@C@FF?EDGFDHH@HGHIIGEGIIIIIEDIIGIIIGHHHIIIIIIIIIII
@HWI-ST273:296:C0EFRACXX:2:1207:14316:145263/1
AATACACCCAACCAGAAGTTAGCTCCTTCGCTTTCAGCTAAATAAAAGCC
+
CCCFFFFFHHHHHJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJIJ

I

I'm interested just about the line that starts with '@HWI', but I want to count all the lines that are not starting with '@HWI'. In the example shown, the result will be 1 because there's one line that starts with '@BBB'.

To be more clear: I just want to know know the number of the first line of the patterns (that are 4 line that repeated) that are not '@HWI'; I hope I'm clear enough. Please tell me if you need more clarification

Please, use the code formatting for the data, not blockquote, so we can see where the lines start and end. — choroba, Apr 23 '20 at 20:06
There is no line that starts with `@BBB`. Do you mean to say "Of all the lines that start with `@`, I want to count how many do not start with `@HWI`?" That's what I think you mean, but if so please update your question with that. And kindly show your attempts. — Quasímodo, Apr 23 '20 at 20:20

score 0 · Answer 1 · answered Apr 24 '20 at 00:41

With GNU sed, you can use its extended address to print every fourth line, then use grep to count the ones that don't start with @HWI:

sed -n '1~4p' file.fastq | grep -cv '^@HWI'

Otherwise, you can use e.g. Perl

perl -ne 'print if 1 == $. % 4' -- file.fastq | grep -cv '^@HWI'

$. contains the current line number, % is the modulo operator.

But once we're running Perl, we don't need grep anymore:

perl -lne '++$c if 1 == $. % 4; END { print $c }' -- file.fastq

-l removes newlines from input and adds them to output.

Counting specific lines that don't contain specific word

1 Answers1