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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 303035201 by Aurimas on Thursday 16th of May 2019 11:33:38 AM
Old 05-16-2019
Help on passing an input variable to the voronota program (after third pipe)

Dear UNIX forum members,

I am using macbook pro 13 (2015 edition) with MAC OS Mojave and am trying to write the shell script where when it is run through terminal it asks for an input (in the code below an input variable is domains) and then that input becomes capital letter or letters which voronota program requires (so instead of 'c<domains>' it should be 'c<C,D>' or any other letter combinations when the voronota program is run at the third pipe). The code is given below :

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 am expecting to get 1.18715 after awk prints the value to the terminal, but in the above code I do not get any value which signals to me that when I write C,D after shell asks "Domains: " the written input is not passed to the variable domain at:

Code:
... | voronota query-contacts --match-first 'c<$domains>' --match-second 'R<ALA>' ...

I will look forward to your help.

Sincerely,
Aurimas

P.S. I tried writing "$domains" but still no success

Last edited by Aurimas; 05-16-2019 at 12:44 PM..
 

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

NAME
pipe -- create descriptor pair for interprocess communication LIBRARY
Standard C Library (libc, -lc) SYNOPSIS
#include <unistd.h> int pipe(int fildes[2]); int pipe2(int fildes[2], int flags); 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. The pipe2() function behaves exactly like pipe() only it allows extra flags to be set on the returned file descriptor. The following flags are valid: O_CLOEXEC Set the ``close-on-exec'' property. O_NONBLOCK Sets non-blocking I/O. O_NOSIGPIPE Return EPIPE instead of raising SIGPIPE. 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() and pipe2() calls will fail if: [EFAULT] The fildes buffer is in an invalid area of the process's address space. The reliable detection of this error cannot be guaranteed; when not detected, a signal may be delivered to the process, indicating an address violation. [EMFILE] Too many descriptors are active. [ENFILE] The system file table is full. pipe2() will also fail if: [EINVAL] flags is other than O_NONBLOCK or O_CLOEXEC. SEE ALSO
sh(1), fork(2), read(2), socketpair(2), write(2) STANDARDS
The pipe() function conforms to ISO/IEC 9945-1:1990 (``POSIX.1''). HISTORY
A pipe() function call appeared in Version 6 AT&T UNIX. The pipe2() function is inspired from Linux and appeared in NetBSD 6.0. BSD
January 23, 2012 BSD
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