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Full Discussion: Redirect string from bash stderr to user stdin
Top Forums Shell Programming and Scripting Redirect string from bash stderr to user stdin Post 302998284 by fredestet on Monday 29th of May 2017 05:45:29 AM
Old 05-29-2017
OK, I'm convinced and will try to explain in more detail. The command in question is called gmx genion from the Gromacs package for molecular dynamics simulations. When executing it in a bash terminal, it prints (using stderr) something like
Code:
Select a continuous group of solvent molecules
Group     0 (         System) has 51133 elements
Group     1 (        Protein) has  3961 elements
Group     2 (      Protein-H) has  1951 elements
Group     3 (        C-alpha) has   244 elements
Group     4 (       Backbone) has   732 elements
Group     5 (      MainChain) has   977 elements
Group     6 (   MainChain+Cb) has  1211 elements
Group     7 (    MainChain+H) has  1215 elements
Group     8 (      SideChain) has  2746 elements
Group     9 (    SideChain-H) has   974 elements
Group    10 (    Prot-Masses) has  3961 elements
Group    11 (    non-Protein) has 47172 elements
Group    12 (          Other) has    44 elements
Group    13 (            UNK) has    44 elements
Group    14 (          Water) has 47128 elements
Group    15 (            SOL) has 47128 elements
Group    16 (      non-Water) has  4005 elements
Select a group:

expecting me to type one of the numbers and hit ENTER. I would always choose the number associated with the group SOL, hence 15 in this particular case. However, this number can vary and I want to automate this step in a bash script where, currently, I execute gmx genion twice:
Code:
groupselect=$(echo "" | gmx genion -s $manyArgs 2>&1 > /dev/null | awk '/ SOL\) has.*elements$/ {print $2}')
echo $groupselect | gmx genion -s $manyArgs 2>&1

The first line stores the string "15" in the variable called $groupselect whereas the second call executes the tool as desired with the content of $groupselect as input. Now, I would like to avoid one of the two calls to gmx genion. Is there a way to get this job done with a single call of gmx genion?

Thanks so far for your efforts!
 

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LEARN ABOUT DEBIAN

rt::client::rest::group

RT::Client::REST::Group(3pm)				User Contributed Perl Documentation			      RT::Client::REST::Group(3pm)

NAME

       RT::Client::REST::Group -- group object representation.

SYNOPSIS

	 my $rt = RT::Client::REST->new(server => $ENV{RTSERVER});

	 my $group = RT::Client::REST::Group->new(
	   rt  => $rt,
	   id  => $id,
	 )->retrieve;

DESCRIPTION

       RT::Client::REST::Group is based on RT::Client::REST::Object.  The representation allows one to retrieve, edit, and create groups in RT.

       Note: RT currently does not allow REST client to search groups.

ATTRIBUTES

       id
	 For retrieval, you can specify either the numeric ID of the group or his group name.  After the retrieval, however, this attribute will
	 be set to the numeric id.

       name
	 Name of the group

       description
	 Description

       members
	 List of the members of this group.

DB METHODS

       For full explanation of these, please see "DB METHODS" in RT::Client::REST::Object documentation.

       retrieve
	 Retrieve RT group from database.

       store
	 Create or update the group.

       search
	 Currently RT does not allow REST clients to search groups.

INTERNAL METHODS

       rt_type
	 Returns 'group'.

SEE ALSO

       RT::Client::REST, RT::Client::REST::Object, RT::Client::REST::SearchResult.

AUTHOR

       Miquel Ruiz <mruiz@cpan.org>

LICENSE

       Perl license with the exception of RT::Client::REST, which is GPLed.

perl v5.14.2							    2012-01-20					      RT::Client::REST::Group(3pm)
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