Counting speceficspecific lines that dosen't conaint speceficdon't contain specific word

Question

[Bioinfo]

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

[WouterDeCoster]

Counting speceficspecific lines that dosen't conaint speceficdon't contain specific word

Please take another look at your title.

[Pierre Lindenbaum]

What have you tried ?

You already asked several question on this site. Please review the correct answers and validate them (green mark on the left).

Answer 1

[Alex Reynolds]

Given test input:

$ cat test.fq
@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

Then you can use awk to filter out the first line of each FASTQ record, test if it does not start with @HWI, and count any of the remaining lines with wc -l:

$ awk '((NR % 4 == 1) && ($1 !~ /^@HWI/))' test.fq | wc -l
       1

If you want to see what those lines are, remove wc -l:

$ awk '((NR % 4 == 1) && ($1 !~ /^@HWI/))' test.fq
@BBBB-ST273:296:C0EFRACXX:2:1303:5281:183410/1

This assumes all your FASTQ records are in standard, four-line blocks.

[Ram]

Would it be better to anchor the regex using ^?

[Alex Reynolds]

Ah yes, will fix that now.