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Full Discussion: awk command in script gives error while same awk command at prompt runs fine: Why?
Top Forums Shell Programming and Scripting awk command in script gives error while same awk command at prompt runs fine: Why? Post 302455063 by catalys on Monday 20th of September 2010 05:08:18 PM
Old 09-20-2010
awk command in script gives error while same awk command at prompt runs fine: Why?
Hello all,

Here is what my bash script does: sums number columns, saves the tot in new column, outputs if tot >= threshold val:

Code:
> cat getnon0file.sh
#!/bin/bash
this="getnon0file.sh"
USAGE=$this" [filename threshold_value]
InFile="xyz.38"
Min="0.05"
#[ I removed the input check to shorten the code]

awk '{sum=0; for(n=2; n<=NF; n++){sum+=$n}; tot=(NF+1);$tot=sum; if(sum>=0.05); {print}}' $InFile > $InFile.non0

echo ----  $this over ---  Result saved into $InFile.non0

When I call the script at the prompt, I get an error:
Code:
> getnon0file.sh xyz.38 0.05
/path/getnon0file.sh: line 36: syntax error near unexpected token `('
/path/getnon0file.sh: line 36: `awk '{sum=0; for(n=2; n<=NF; n++){sum+=$n}; tot=(NF+1);$tot=sum; if(sum>=0.05); {print}}' $InFile > 
$InFile.non0'

When I run the awk command alone at the prompt, I obtain the results I want
Code:
> awk '{sum=0; for(n=2; n<=NF; n++){sum+=$n}; tot=(NF+1);$tot=sum; if(sum>=0.05); {print}}' xyz.38 > xyz.38.non0

Is there any way around what seems to me an attractable error?

Thanks.

Just in case you need it, the datafile (xyz.38) look like this:

Code:
code1_001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.008 0.028 0.198 0.502 0.625
code1_002 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.009 0.066 0.158 0.190
code1_003 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.009 0.060 0.148 0.185
code1_004 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 0.992 0.954 0.676 0.192 0.000
code2_001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.008 0.055 0.229 0.390
code2_002 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004 0.024 0.108 0.193
code2_003 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.029 0.118 0.209

Last edited by radoulov; 09-20-2010 at 06:14 PM.. Reason: Code tags, please!
 

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LEARN ABOUT NETBSD

usleep

USLEEP(3)						   BSD Library Functions Manual 						 USLEEP(3)

NAME

     usleep -- suspend execution for interval of microseconds

LIBRARY

     Standard C Library (libc, -lc)

SYNOPSIS

     #include <unistd.h>

     int
     usleep(useconds_t microseconds);

DESCRIPTION

     The usleep() function suspends execution of the calling process until either the number of microseconds specified by microseconds have
     elapsed or a signal is delivered to the calling process and its action is to invoke a signal catching function or to terminate the process.
     The suspension time may be longer than requested due to the scheduling of other activity by the system.

     The microseconds argument must be less than 1,000,000.  If the value of microseconds is 0, then the call has no effect.

RETURN VALUES

     On successful completion, usleep() returns 0.  Otherwise, it returns -1 and sets errno to indicate the error.

ERRORS

     The usleep() function may fail if:

     [EINVAL]		The microseconds interval specified 1,000,000 or more microseconds.

SEE ALSO

     nanosleep(2), sleep(3)

STANDARDS

     The usleep() function conforms to X/Open Portability Guide Issue 4, Version 2 (``XPG4.2'').  It later appeared in the POSIX standard, but in
     IEEE Std 1003.1-2004 (``POSIX.1'') it was marked as legacy and the use of nanosleep(2) was recommended instead.  The IEEE Std 1003.1-2008
     (``POSIX.1'') revision removed usleep() from the specification.

HISTORY

     The usleep() function appeared in 4.3BSD.

BSD
								  April 29, 2010							       BSD
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