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An Ignorant Wanderer
Asked: 2020-07-08 15:41:08 +0800 CST

Hyphen in egrep [duplicate]

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I run the following command in bash:

echo "#fastq-dump SRR3105676 --gzip -O my &" | egrep "-O"

and I get

grep: invalid option -- 'O'
Usage: grep [OPTION]... PATTERNS [FILE]...
Try 'grep --help' for more information.

I understand that to fix this I need to escape the hyphen (dash) in the quotes, but why is this happening? Why is the shell interpreting the "-O" as an option and not as a regex?

command-line bash grep

1 Answers

  1. Best Answer

    The shell isn't interpreting anything - it's simply passing -O (after quote removal) to the grep executable, which parses it as part of its argument vector argv[]

    You can either signal the end of options using --

    echo "#fastq-dump SRR3105676 --gzip -O my &" | egrep -- "-O"

    or (for the case of grep specifically) use the -e option (or its long form --regexp) to explicitly tell it that the next argument is an expression:

    echo "#fastq-dump SRR3105676 --gzip -O my &" | egrep -e "-O"

    From man grep:

       -e PATTERN, --regexp=PATTERN
          Use PATTERN as the pattern.  If this  option  is  used  multiple
          times or is combined with the -f (--file) option, search for all
          patterns given.  This option can be used to  protect  a  pattern
          beginning with “-”.
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