Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: perl: Command works in terminal, but not in shell script
Top Forums Shell Programming and Scripting perl: Command works in terminal, but not in shell script Post 302801755 by jdilts on Thursday 2nd of May 2013 01:26:17 PM
Old 05-02-2013
colon after while block ... still produces the same error
Thanks balajesuri, but even with the fix, I still got the same error.

What I found interesting was the command echoed from the 'run' statement. They aren't identical (aside from the file names).

script command
Code:
samtools view -h rawlib.bam | perl -ne '{ @line = split( /\s+/ ); $match = 0; while( $line[5] =~ /(\d+)M/g ) { $match= $match + $1 } if( $match >= 80 || $_ =~ /^\@/ ) { print $_ } }' | java -Xmx12G -jar /opt/picard/picard-tools-current/SortSam.jar I=/dev/stdin O=rawlib.gt80.bam VERBOSITY=WARNING QUIET=TRUE SO=coordinate; samtools index rawlib.gt80.bam

echoed command
Code:
samtools view -h /results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_rawlib.bam | perl -ne '{ @line = split( /\s+/ );  = 0; while( runplugin/runlevel	""[5] =~ /(\d+)M/g ) {  =  + -j }if(  >= 80 || /results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_oldrawlib.bam =~ /^\@/ ) { print /results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_oldrawlib.bam } }' | java -Xmx12G -jar /opt/picard/picard-tools-current/SortSam.jar I=/dev/stdin O=/results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_rawlib.bam VERBOSITY=WARNING QUIET=TRUE SO=coordinate

It looks like the variable $match isn't being created? I'm just trying to shed some light on what might be the problem....
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

perl - how come this script works?

#!/usr/bin/perl open (DATA, file.txt); @array = <DATA>; close (DATA); open (DATA, ">$file.txt"); for (@array) { s/text/replace text/; push(@contents,$_); } seek(DATA, 0, 0); print DATA (@contents); close(DATA); could someone please explain how this works. i've been... (3 Replies)
Discussion started by: mjays
3 Replies

2. Shell Programming and Scripting

#!/bin/bash and #1bin/sh command not found error on mac osx terminal/shell script

i am having a weird error on mac os x running some shell scripts. i am a complete newbie at this and this question concerns 2 scripts. one of which a friend of mine wrote (videochecker.sh) a couple weeks ago and it's been running fine on another machine. then last week i wrote capture.sh and it... (2 Replies)
Discussion started by: danpaluska
2 Replies

3. Shell Programming and Scripting

perl/unix: script in command line works but not in perl

so in unix this command works works and shows me a list of directories find . -name \*.xls -exec dirname {} \; | sort -u | > list.txt but when i try running a perl script to run this command my $query = 'find . -name \*.xls -exec dirname {} \; | sort -u | > list.txt';... (2 Replies)
Discussion started by: kpddong
2 Replies

4. Shell Programming and Scripting

how the typeset command works in shell script

typeset -l section section=${2:-.} what does these 2 lines meaning? (1 Reply)
Discussion started by: venkatababu
1 Replies

5. Shell Programming and Scripting

help with shell script: cp command not working, but mv command works...

Hello. I would like to ask your help regarding the cp command. We are using a cp command to create a back-up copy of our file but to no avail. It's just not working. We already checked the file and directory permissions and all seems correct. We have a script (ftp.script) which calls on... (1 Reply)
Discussion started by: udelalv
1 Replies

6. Shell Programming and Scripting

SED command works in terminal, but not Applescript

The following command works perfectly in Terminal, but not in Applescript. (Returns "unknown token" error for square brackets.) (new to site. sorry.) I have an Applescript that is designed to find and remove any square-bracketed text, including the square brackets. I ran the following code from... (1 Reply)
Discussion started by: Phillip Acosta
1 Replies

7. UNIX for Dummies Questions & Answers

Shell script not working but command works in command prompt

Hi everyone I have a problem with my script If I try directly this command /usr/bin/nice -n 19 mysqldump -u root --password="******" wiki_schneider -c | nice -n 19 gzip -9 > /point_de_montage/$(date '+%Y%m%d')-wiki-db.sql.gz It works But if I simply add this command in a script and... (8 Replies)
Discussion started by: picemma
8 Replies

8. Shell Programming and Scripting

Perl error in batch command but works one at a time

In the below perl executes if one file is processed perfect. However, when multiple files are processed in batch which is preferred I get the below error that I can not seem to fix it as the '' necessary for the command to execute, but seem to only work for one -arg option. Thank you :). ... (2 Replies)
Discussion started by: cmccabe
2 Replies

9. Shell Programming and Scripting

Need to understand how the line in perl program works as shell commend

I have a file with two line, one is header, the other actual value: TYPCD|ETID2|ETID|LEG ID|PTYP|PTYP SUB|TRD STATUS|CXL REASON|CACT|CACTNM|ENCD|ENC D NM|TRDR|ASDT|TRDT|MTDT|STDT|LS|SECID|SECID TYP|SECNM|PAR|STCC|MARKET PRICE|DIS MARKET PRICE|MARKET PRICE CURRENCY|SRC OF SETTLEMENT... (2 Replies)
Discussion started by: digioleg54
2 Replies

10. Shell Programming and Scripting

Replace string works on command-line but fails when run from shell script

I wish to replace "\\n" with a single white space. The below does the job on command-line: $ echo '/fin/app/scripts\\n/fin/app/01/sql' | sed -e 's#\\\\n# #g'; /fin/app/scripts /fin/app/01/sql However, when i have the same code to a shell script it is not able to get me the same output:... (8 Replies)
Discussion started by: mohtashims
8 Replies

LEARN ABOUT REDHAT

set_color

set_color(1)							       fish							      set_color(1)

NAME

       set_color - set_color - set the terminal color

set_color - set the terminal color
   Synopsis
       set_color [-v --version] [-h --help] [-b --background COLOR] [COLOR]

   Description
       Change the foreground and/or background color of the terminal. COLOR is one of black, red, green, brown, yellow, blue, magenta, purple,
       cyan, white and normal.

       o -b, --background Set the background color

       o -c, --print-colors Prints a list of all valid color names

       o -h, --help Display help message and exit

       o -o, --bold Set bold or extra bright mode

       o -u, --underline Set underlined mode

       o -v, --version Display version and exit

       Calling set_color normal will set the terminal color to whatever is the default color of the terminal.

       Some terminals use the --bold escape sequence to switch to a brighter color set. On such terminals, set_color white will result in a grey
       font color, while set_color --bold white will result in a white font color.

       Not all terminal emulators support all these features. This is not a bug in set_color but a missing feature in the terminal emulator.

       set_color uses the terminfo database to look up how to change terminal colors on whatever terminal is in use. Some systems have old and
       incomplete terminfo databases, and may lack color information for terminals that support it. Download and install the latest version of
       ncurses and recompile fish against it in order to fix this issue.

Version 1.23.1							  Sun Jan 8 2012						      set_color(1)
All times are GMT -4. The time now is 07:45 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy