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Top Forums Shell Programming and Scripting Remove or rename based on contents of file Post 302943653 by cmccabe on Monday 11th of May 2015 01:20:55 PM
Old 05-11-2015
I hope this is more clear:
I am trying to use the two files shown below to either remove or rename contents in one of those files. If in combine.txt $5 matches $5 of output.txt and the value in $1 of combine.txt is not "No Match" then that value is substituted for all values in $5 and $1 of output.txt. If however in $1 of combine.txt the value is "No Match", then the row in output.txt with that $5 value in it and the one below it are removed. Thank you Smilie.

For example,
"DTE3504500000004" is the value of $5 in combine.txt and that matches row 3 of output.txt $5 , since the value in $1 of combine.txt is "No Match", rows 9 and 10 are removed from output.txt.

"DTE3504500000005" is the value of $5 in combine.txt and that matches row 11 of output.txt $5 , since the value in $1 of combine.txt is not "No Match", rather "PXL-A0000005" that new value is used to replace all occurrences of the old value in output.txt.

Code:
file1.txt
No Match    chr1    35696    36106    DTE3504500000004
PXL-A0000005    chr1    69066    69311    DTE3504500000005

Code:
Initial output.txt:
RefPrimer    ref    antiref    omosome    PrimerSet    SeqRxn
AntirefPrimer    antiref    ref    omosome        
DTE3504500000001ref    34529    35031    1    DTE3504500000001    SeqRxn4
DTE3504500000001antiref    35031    34529    1        
DTE3504500000002ref    35032    35283    1    DTE3504500000002    SeqRxn4
DTE3504500000002antiref    35283    35032    1        
DTE3504500000003ref    35284    35506    1    DTE3504500000003    SeqRxn4
DTE3504500000003antiref    35506    35284    1        
DTE3504500000004ref    35696    36106    1    DTE3504500000004    SeqRxn4
DTE3504500000004antiref    36106    35696    1        
DTE3504500000005ref    69066    69311    1    DTE3504500000005    SeqRxn4
DTE3504500000005antiref    69311    69066    1

Code:
Desired output.txt:
RefPrimer    ref    antiref    omosome    PrimerSet    SeqRxn
AntirefPrimer    antiref    ref    omosome        
DTE3504500000001ref    34529    35031    1    DTE3504500000001    SeqRxn4
DTE3504500000001antiref    35031    34529    1        
DTE3504500000002ref    35032    35283    1    DTE3504500000002    SeqRxn4
DTE3504500000002antiref    35283    35032    1        
DTE3504500000003ref    35284    35506    1    DTE3504500000003    SeqRxn4
DTE3504500000003antiref    35506    35284    1        
PXL-A0000005ref    69066    69311    1    PXL-A0000005    SeqRxn4
PXL-A0000005antiref    69311    69066    1


Last edited by cmccabe; 05-11-2015 at 03:09 PM..
 

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PARALLEL-SLURP(1)														 PARALLEL-SLURP(1)

NAME
parallel-slurp - copy files from listed hosts SYNOPSIS
parallel-slurp [OPTIONS] -h hosts.txt -L destdir remote local DESCRIPTION
pssh provides a number of commands for executing against a group of computers, using SSH. It's most useful for operating on clusters of homogenously-configured hosts. parallel-slurp gathers specified files from hosts you listed. OPTIONS
-r --recursive recusively copy directories (OPTIONAL) -L --localdir output directory for remote file copies -h --hosts hosts file (each line "host[:port] [user]") -l --user username (OPTIONAL) -p --par max number of parallel threads (OPTIONAL) -o --outdir output directory for stdout files (OPTIONAL) -e --errdir output directory for stderr files (OPTIONAL) -t --timeout timeout (secs) (-1 = no timeout) per host (OPTIONAL) -O --options SSH options (OPTIONAL) -v --verbose turn on warning and diagnostic messages (OPTIONAL) EXAMPLE
An example to copy /home/irb2/foo.txt from each host. Files gathered will be stored in /tmp/outdir/hostname/foo.txt. # prallel-slurp -h hosts.txt -L /tmp/outdir -l irb2 /home/irb2/foo.txt foo.txt ENVIRONMENT
All four programs take similar sets of options. All of these options can be set using the following environment variables: o PSSH_HOSTS o PSSH_USER o PSSH_PAR o PSSH_OUTDIR o PSSH_VERBOSE o PSSH_OPTIONS SEE ALSO
parallel-ssh(1), parallel-scp(1), parallel-nuke(1), parallel-rsync(1), ssh(1) AUTHOR
Brent N. Chun <bnc@theether.org> COPYING
Copyright: 2003, 2004, 2005, 2006, 2007 Brent N. Chun NOTES
1. bnc@theether.org mailto:bnc@theether.org 03/30/2009 PARALLEL-SLURP(1)
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