Sponsored Content
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
SCRIPT(1)						    BSD General Commands Manual 						 SCRIPT(1)

NAME
script -- make typescript of terminal session SYNOPSIS
script [-a] [-k] [-q] [-t time] [file [command ...]] DESCRIPTION
The script utility makes a typescript of everything printed on your terminal. It is useful for students who need a hardcopy record of an interactive session as proof of an assignment, as the typescript file can be printed out later with lpr(1). If the argument file is given, script saves all dialogue in file. If no file name is given, the typescript is saved in the file typescript. If the argument command ... is given, script will run the specified command with an optional argument vector instead of an interactive shell. Options: -a Append the output to file or typescript, retaining the prior contents. -k Log keys sent to program as well as output. -q Run in quiet mode, omit the start and stop status messages. -t time Specify time interval between flushing script output file. A value of 0 causes script to flush for every character I/O event. The default interval is 30 seconds. The script ends when the forked shell (or command) exits (a control-D to exit the Bourne shell (sh(1)), and exit, logout or control-d (if ignoreeof is not set) for the C-shell, csh(1)). Certain interactive commands, such as vi(1), create garbage in the typescript file. The script utility works best with commands that do not manipulate the screen. The results are meant to emulate a hardcopy terminal, not an addressable one. ENVIRONMENT
The following environment variable is utilized by script: SHELL If the variable SHELL exists, the shell forked by script will be that shell. If SHELL is not set, the Bourne shell is assumed. (Most shells set this variable automatically). SEE ALSO
csh(1) (for the history mechanism). HISTORY
The script command appeared in 3.0BSD. BUGS
The script utility places everything in the log file, including linefeeds and backspaces. This is not what the naive user expects. It is not possible to specify a command without also naming the script file because of argument parsing compatibility issues. When running in -k mode, echo cancelling is far from ideal. The slave terminal mode is checked for ECHO mode to check when to avoid manual echo logging. This does not work when in a raw mode where the program being run is doing manual echo. BSD
June 6, 1993 BSD
All times are GMT -4. The time now is 10:48 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy