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Top Forums UNIX for Beginners Questions & Answers Help on passing an input variable to the voronota program (after third pipe) Post 303035224 by Aurimas on Thursday 16th of May 2019 03:26:26 PM
Old 05-16-2019
Dear all,

How can I exit the script and return to terminal if domains is not equal to .pdb file, which i specifies . How could I make domains to be equal to "e" or any other string, number, etc. that would mean for the script to exit it and return to terminal?

The upgraded script:
Code:
#!/bin/bash
for i in $( ls ); do
    echo $i
    read -p "Domains: " domains
    cat $i | voronota get-balls-from-atoms-file --annotated | voronota calculate-contacts --annotated | voronota query-contacts --match-first "'c<$domains>'" --match-second 'R<ALA>' | awk '{sum += $3} END {print sum}'
done

I will look forward to your replies.

Sincerely,
Aurimas

--- Post updated at 07:26 PM ---

Solved. No need for help.

Last edited by Aurimas; 05-16-2019 at 04:26 PM..
 

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PIPE(2) 						      BSD System Calls Manual							   PIPE(2)

NAME
pipe -- create descriptor pair for interprocess communication SYNOPSIS
#include <unistd.h> int pipe(int *fildes); DESCRIPTION
The pipe() function creates a pipe, which is an object allowing unidirectional data flow, and allocates a pair of file descriptors. The first descriptor connects to the read end of the pipe, and the second connects to the write end, so that data written to fildes[1] appears on (i.e., can be read from) fildes[0]. This allows the output of one program to be sent to another program: the source's standard output is set up to be the write end of the pipe, and the sink's standard input is set up to be the read end of the pipe. The pipe itself persists until all its associated descriptors are closed. A pipe whose read or write end has been closed is considered widowed. Writing on such a pipe causes the writing process to receive a SIGPIPE signal. Widowing a pipe is the only way to deliver end-of-file to a reader: after the reader consumes any buffered data, reading a widowed pipe returns a zero count. RETURN VALUES
On successful creation of the pipe, zero is returned. Otherwise, a value of -1 is returned and the variable errno set to indicate the error. ERRORS
The pipe() call will fail if: [EMFILE] Too many descriptors are active. [ENFILE] The system file table is full. [EFAULT] The fildes buffer is in an invalid area of the process's address space. SEE ALSO
sh(1), read(2), write(2), fork(2), socketpair(2) HISTORY
A pipe() function call appeared in Version 6 AT&T UNIX. 4th Berkeley Distribution June 4, 1993 4th Berkeley Distribution
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