Why does my grep command output "--" between some lines?

Question

I have a fasta file like the test one here:

>HWI-D00196:168:C66U5ANXX:3:1106:16404:19663 1:N:0:GCCAAT
CCTAGCACCATGATTTAATGTTTCTTTTGTACGTTCTTTCTTTGGAAACTGCACTTGTTGCAACCTTGCAAGCCATATAAACACATTTCAGATATAAGGCT
>HWI-D00196:168:C66U5ANXX:3:1106:16404:19663 2:N:0:GCCAAT
AAAACATAAATTTGAGCTTGACAAAAATTAAAAATGAGCCCAGCCTTATATCTGAAATGTGTTTATATGGCTTGCAAGGTTGCAACAAGTGCAGTTTCCAA
>HWI-D00196:168:C66U5ANXX:4:1304:10466:100132 1:N:0:GCCAAT
ATATTTGAATTATCAGAAATAAACACAAAGAAAACCTAGAACAGATAATTTCTTCCACATTATTGATCAGATACAGATTTCAAGGGTACCGTTGTGAATTG
>HWI-D00196:168:C66U5ANXX:4:1304:10466:100132 2:N:0:GCCAAT
AAACGATTGATAGATCTATTTGCATTATAAAAACATTAAAAAAACAAAATACTGATTAAATGTCGTCTTTCTATTCCACAATTTTATAGATCTCACTGTAT
>HWI-D00196:168:C66U5ANXX:4:1307:12056:64030 1:N:0:GCCAAT
CTTACTTTGCCTCTCTCAGCCAATGTCTCCTGAGTCTAATTTTTTGGAGGCTAAGCTATGAGCTAATGATGGGTTCCATTTGGGGCCAATGCTTCAGCCTG
>HWI-D00196:168:C66U5ANXX:4:1307:12056:64030 2:N:0:GCCAAT
CTATTAGTTCTTATCTTTGCCTGCAAATATAAGACTAGCGCTTGAGTAGCTGACAGAGACAAAGTAAGCTGGAGTGTTTATCACCTGGTCACTCCAATTGT

When i type in a simple grep command like:

grep -B1 "CTT" test.fasta

I get a really strange output in which "--" is sometimes placed on a newline above the grep hit like so:

>HWI-D00196:168:C66U5ANXX:4:1304:10466:100132 2:N:0:GCCAAT
AAACGATTGATAGATCTATTTGCATTATAAAAACATTAAAAAAACAAAATACTGATTAAATGTCGTCTTTCTATTCCACAATTTTATAGATCTCACTGTAT
--
>HWI-D00196:168:C66U5ANXX:4:1307:12056:64030 2:N:0:GCCAAT
CTATTAGTTCTTATCTTTGCCTGCAAATATAAGACTAGCGCTTGAGTAGCTGACAGAGACAAAGTAAGCTGGAGTGTTTATCACCTGGTCACTCCAATTGT

I can't figure out why some fasta entries have this and others don't. I don't get this problem when i remove the -B1. I can remove those lines from my file with a grep -v "--" statement, but I'd really like to understand what's going on here.

Answer 1

You are asking for one line of leading context by using the -B1 option. This means grep will display both the line which matched and the line directly before it. Each match will be separated by -- on a line by itself as shown below:

$ man grep | grep -B1 context
     -A num, --after-context=num
             Print num lines of trailing context after each match.  See also
--
     -B num, --before-context=num
             Print num lines of leading context before each match.  See also
--
     -C[num, --context=num]
             Print num lines of leading and trailing context surrounding each
--
     --context[=num]
             Print num lines of leading and trailing context.  The default is

The reason you aren't seeing -- between every match is that the context is only displayed above a sequence of consecutive matches. So see the following example:

seq 13 | grep -B1 1
1
--
9
10
11
12
13

The seq command produces all the numbers between 1 and 13. Only the first line and the lines from 10 on contain a 1, so you see the 1 in its own group, then --, then the one line context, then the group of consecutive matching lines.