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Top Forums Shell Programming and Scripting Program to match the id and replace one letter in the content Post 302840179 by kaav06 on Monday 5th of August 2013 12:30:44 AM
Old 08-05-2013
Program to match the id and replace one letter in the content

Hi all,
I have one file with a sequence and the other file which says the position and the letter to be changed. I have to match two files and replace content. Example is shown which will describe what I want to do. For example, file 1 has many sequences and few are shown below

sequence file:
Code:
>sp|P78363|ABCA4_HUMAN Retinal-specific ATP-binding cassette transporter OS=Homo sapiens GN=ABCA4 PE=1 SV=3
MGFVRQIQLLLWKNWTLRKRQKIRFVVELVWPLSLFLVLIWLRNANPLYSHHECHFPNKA
MPSAGMLPWLQGIFCNVNNPCFQSPTPGESPGIVSNYNNSILARVYRDFQELLMNAPESQ
>sp|P21439|MDR3_HUMAN Multidrug resistance protein 3 OS=Homo sapiens GN=ABCB4 PE=1 SV=2
MDLEAAKNGTAWRPTSAEGDFELGISSKQKRKKTKTVKMIGVLTLFRYSDWQDKLFMSLG
TIMAIAHGSGLPLMMIVFGEMTDKFVDTAGNFSFPVNFSLSLLNPGKILEEEMTRYAYYY

and the second file has the id which is enclosed in between || in the first file and the letters to be changed. Now I have to match the id column with the header line in the seuqence file |P78363|. if they are same, do the change as mentioned and write in the output file.
Code:
Id         Orginial letter Position to be chnaged to 
P78363        M              1             T
P78363        G              2              E
P21439        L               3              A

the output file should contain the sequences of the changed letters and the change name in the header as highlighted (bold) in the below code
Code:
>sp|P78363|M1T ABCA4_HUMAN Retinal-specific ATP-binding cassette transporter OS=Homo sapiens GN=ABCA4 PE=1 SV=3
TGFVRQIQLLLWKNWTLRKRQKIRFVVELVWPLSLFLVLIWLRNANPLYSHHECHFPNKA
MPSAGMLPWLQGIFCNVNNPCFQSPTPGESPGIVSNYNNSILARVYRDFQELLMNAPESQ
>sp|P78363|G2E ABCA4_HUMAN Retinal-specific ATP-binding cassette transporter OS=Homo sapiens GN=ABCA4 PE=1 SV=3
MEFVRQIQLLLWKNWTLRKRQKIRFVVELVWPLSLFLVLIWLRNANPLYSHHECHFPNKA
MPSAGMLPWLQGIFCNVNNPCFQSPTPGESPGIVSNYNNSILARVYRDFQELLMNAPESQ
>sp|P21439|L3A MDR3_HUMAN Multidrug resistance protein 3 OS=Homo sapiens GN=ABCB4 PE=1 SV=2
MDAEAAKNGTAWRPTSAEGDFELGISSKQKRKKTKTVKMIGVLTLFRYSDWQDKLFMSLG
TIMAIAHGSGLPLMMIVFGEMTDKFVDTAGNFSFPVNFSLSLLNPGKILEEEMTRYAYYY

Could anyone please help with a script which can do this. It will be bery helpful
Note: this is not a school exercise.

Thanks
Kaavya
 

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replace(1)							  MySQL database							replace(1)

NAME
replace - A utility program that is used by msql2mysql, but that has more general applicability as well. replace changes strings in place in files or on the standard input. Uses a finite state machine to match longer strings first. Can be used to swap strings. USAGE
replace [-?svIV] from to from to ... -- [files] or replace [-?svIV] from to from to ... < fromfile > tofile SYNOPSIS
replace [-?|-I] [-s] [-v] DESCRIPTION
replace -?|-I info -s silent -v verbose EXTRA INFO
Special characters in from string: ^ Match start of line. $ Match end of line.  Match space-character, start of line or end of line. For a end  the next replace starts locking at the end space-character. A  alone in a string matches only a space-character. EXAMPLE
this command swaps a and b in the given files: shell> replace a b b a -- file1 file2 ... SEE ALSO
isamchk(1), isamlog(1), mysql(1), mysqlaccess(1), mysqladmin(1), mysqld(1), mysqld_multi(1), mysqld_safe(1), mysqldump(1), mysql_fix_privi- lege_tables(1), mysqlshow(1), mysql_zap(1), perror(1), For more information please refer to the MySQL reference manual, which may already be installed locally and which is also available online at http://www.mysql.com/doc/en/ BUGS
Please refer to http://bugs.mysql.com/ to report bugs. AUTHOR
Ver 1.0, distribution 4.0.24 Michael (Monty) Widenius (monty@mysql.com), MySQL AB (http://www.mysql.com/). This software comes with no warranty. Manual page by L. (Kill-9) Pedersen (kill-9@kill-9.dk), Mercurmedia Data Model Architect / system developer (http://www.mercur- media.com) ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +--------------------+------------------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +--------------------+------------------------------------+ |Availability | SUNWmysqlr, SUNWmysqlu, SUNWmysqlt | +--------------------+------------------------------------+ |Interface Stability | External | +--------------------+------------------------------------+ NOTES
Source for mysql is available on http://opensolaris.org. MySQL 4.0 19 December 2000 replace(1)
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