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Full Discussion: How to pass a single quote to the program?
Top Forums UNIX for Beginners Questions & Answers How to pass a single quote to the program? Post 303036116 by RudiC on Friday 14th of June 2019 09:29:01 AM
Old 06-14-2019
You definitely need to split your pipeline into single commands and analyse each one of them separately in order to identify what is going wrong. I don't know the voronota command, what it requires, and what its outputs should look like, but piping some file through three instances of it is somewhat new to me.


Re. your single quote question, to me the double quoting seems to do exactly what you need. echoing your third voronota command with the respective variables and quoting yields:
Code:
echo voronota query-contacts --inter-residue --match-first "'R<$AAA>'" --match-second "'A<C1',C2',C3',C4',C5',O1,O2,O3,O4,O5,O1',O2',O3',O4',O5',N1,N2,N3,C1,C2,C3,C4,C5>'" 
voronota query-contacts --inter-residue --match-first 'R<ALA>' --match-second 'A<C1',C2',C3',C4',C5',O1,O2,O3,O4,O5,O1',O2',O3',O4',O5',N1,N2,N3,C1,C2,C3,C4,C5>'

These 2 Users Gave Thanks to RudiC For This Post:
Aurimas Neo
 

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LEARN ABOUT FREEBSD

lessecho

LESSECHO(1)						      General Commands Manual						       LESSECHO(1)

NAME

       lessecho - expand metacharacters

SYNOPSIS

       lessecho [-ox] [-cx] [-pn] [-dn] [-mx] [-nn] [-ex] [-a] file ...

DESCRIPTION

       lessecho  is  a program that simply echos its arguments on standard output.  But any metacharacter in the output is preceded by an "escape"
       character, which by default is a backslash.

OPTIONS

       A summary of options is included below.

       -ex    Specifies "x", rather than backslash, to be the escape char for metachars.  If x is "-", no escape char is used and  arguments  con-
	      taining metachars are surrounded by quotes instead.

       -ox    Specifies "x", rather than double-quote, to be the open quote character, which is used if the -e- option is specified.

       -cx    Specifies "x" to be the close quote character.

       -pn    Specifies "n" to be the open quote character, as an integer.

       -dn    Specifies "n" to be the close quote character, as an integer.

       -mx    Specifies "x" to be a metachar.  By default, no characters are considered metachars.

       -nn    Specifies "n" to be a metachar, as an integer.

       -fn    Specifies "n" to be the escape char for metachars, as an integer.

       -a     Specifies that all arguments are to be quoted.  The default is that only arguments containing metacharacters are quoted

SEE ALSO

       less(1)

AUTHOR

       This manual page was written by Thomas Schoepf <schoepf@debian.org>, for the Debian GNU/Linux system (but may be used by others).

       Send bug reports or comments to bug-less@gnu.org.

							     Version 458: 04 Apr 2013						       LESSECHO(1)
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