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Full Discussion: Replace text in column1 of a file matching columns of another file
Top Forums Shell Programming and Scripting Replace text in column1 of a file matching columns of another file Post 302742657 by thienxho on Tuesday 11th of December 2012 11:51:25 AM
Old 12-11-2012
Replace text in column1 of a file matching columns of another file
Hi all,

I have 2 files:

species-names.txt

Code:
Abaca-bunchy-top-virus	((((Abaca-bunchy-top-virus((Babuvirus((Unassigned((Nanoviridae((Unassigned))))
Abutilon-mosaic-virus	((((Abutilon-mosaic-virus((Begomovirus((Unassigned((Geminiviridae((Unassigned))))
Abutilon-yellows-virus	((((Abutilon-yellows-virus((Crinivirus((Unassigned((Closteroviridae((Unassigned))))

sequence-names.txt

Code:
gi|145845934|gb|EF546810.1|-Abaca-bunchy-top-virus-isolate-Q767-segment-DNA-S,-complete-sequence	GGCAGGGGGGCTTATTATTACCCCCCCTGCC
gi|145845936|gb|EF546811.1|-Abutilon-mosaic-virus-isolate-Q767-segment-DNA-M,-complete-sequence	GGGGCTGGGGCTTATTATTACCCCCAGCCCCGGAACGGGACATCAC
gi|145845938|gb|EF546812.1|-Abutilon-yellows-virus-isolate-Q767-segment-DNA-C,-complete-sequence	GGCAGGGGGGCTTATTATTACCCCCCCTGCCCGGG

I need to replace text in 1st column of file sequence-names.txt which matches 1st column of file species-names.txt to text of 2nd column of species-names.txt. Output will be:

Code:
gi|145845934|gb|EF546810.1|-((((Abaca-bunchy-top-virus((Babuvirus((Unassigned((Nanoviridae((Unassigned))))-isolate-Q767-segment-DNA-S,-complete-sequence	GGCAGGGGGGCTTATTATTACCCCCCCTGCC
gi|145845936|gb|EF546811.1|-((((Abutilon-mosaic-virus((Begomovirus((Unassigned((Geminiviridae((Unassigned))))-isolate-Q767-segment-DNA-M,-complete-sequence	GGGGCTGGGGCTTATTATTACCCCCAGCCCCGGAACGGGACATCAC
gi|145845938|gb|EF546812.1|-((((Abutilon-yellows-virus((Crinivirus((Unassigned((Closteroviridae((Unassigned))))-isolate-Q767-segment-DNA-C,-complete-sequence	GGCAGGGGGGCTTATTATTACCCCCCCTGCCCGGG

Thanks a lot!
 

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LEARN ABOUT DEBIAN

amavisd-new

AMAVISD-NEW(8)						      System Manager's Manual						    AMAVISD-NEW(8)

NAME

       amavisd-new - Interface between MTA and virus scanner/content filters

SYNOPSIS

       amavisd-new [ -u userid ] [ -g groupid ] [ -c config-file ]...  [ start | stop | reload | debug | debug-sa | foreground ]

DESCRIPTION

       amavisd is a high-performance interface between message transfer agent (MTA) and virus scanners and/or spam scanners.

       This is the amavisd-new incarnation of amavisd.	It is a performance-enhanced and feature-enriched version of the original amavisd program.

       Amavisd-new  works  as  a  SMTP	proxy.	Email is fed to it through SMTP, processed, and fed back to the MTA through a new SMTP connection.
       There is no buffering to disk by amavis, it will report that the transfer was sucessfull only after the forwarding  MTA	has  accepted  the
       message.

       It is possible to use the sendmail milter interface instead of the SMTP proxy method, as well.

OPTIONS

       -c configfile
	      Use  the	specified  configuration  file	instead  of  using  run-parts(8)  to  find  config  files  in /usr/share/amavis/conf.d and
	      /etc/amavis/conf.d (this is a Debian extension to Amavisd-new).  More than one -c option can be specified and the files will be read
	      in the order given.

       -u userid
	      Try to switch to that user id.

       -g groupid
	      Try to switch to that group id.

       start  Starts amavisd-new

       stop   Stops a running amavisd-new

       reload Reloads configuration from config file (may in fact just restart amavisd-new)

       debug  Runs amavisd-new in debug mode

       debug-sa
	      Runs amavisd-new in spamassassin debug mode

       foreground
	      Does not fork to background

FILES

       /etc/amavis/amavisd.conf, /var/lib/amavis, /var/run/amavis/amavisd.pid

SEE ALSO

       /usr/share/doc/amavisd-new/*

AUTHOR

       This manual page was written by Henrique de Moraes Holschuh <hmh@debian.org>, for the Debian GNU/Linux system (but may be used by others).

								    2003-01-01							    AMAVISD-NEW(8)
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