Search id from second file and append in first Post: 302887757

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Top Forums Shell Programming and Scripting Search id from second file and append in first Post 302887757 by gina.lizar on Monday 10th of February 2014 04:26:21 PM

02-10-2014

Registered User

Search id from second file and append in first

Hello,

I want to search a string/substring from the second column in file in another file and append the first found record in second file to the end of the record in the first file. Both files are tab delimited.

All lines with KOG in col13 do not need to be searched as it will not be found.

Here the logic in my head which needs to translate into code.

In all lines which does not contain the keyword 'KOG' in the column 13 of file1

Extract substring for searching:when second column has values starting with
sp| or tr| ,, example when value is sp|P32770|NRP1_YEAST , string to be searched is P32770..
when value is tr|N1PNC6|N1PNC6_MYCP1 , string to be searched is N1PNC6

if the second column does not start with sp| or tr| ... it has values like NP_001059837 or AEW46684 then the entire string needs to be searched.

If searched string is found, append the entire first matching line in file2 to the end of the corresponding record in file1 after a tab.

A lot of the second column values repeat, so it would be good if the search for the same value is done only once. For example AEW46684 occurs in the second column of file1 119 times, so searching it just once might save computation with these huge files.

Since there are many columns in the samples I have attached sample inputs and output.

file1_samp.txt (450 Bytes)

file2_samp.txt (722 Bytes)

result1.txt (1.1 KB)

gina.lizar

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script

script(1)							   User Commands							 script(1)

NAME

       script - make record of a terminal session

SYNOPSIS

       script [-a] [filename]

DESCRIPTION

       The  script  utility  makes a record of everything printed on your screen. The record is written to filename. If no file name is given, the
       record is saved in the file typescript. See WARNINGS.

       The script command forks and creates a sub-shell, according to the value of $SHELL, and records the text from this session. The script ends
       when the forked shell exits or when Control-d is typed.

OPTIONS

       The following option is supported:

       -a    Appends the session record to filename, rather than overwriting it.

NOTES

       script places everything that appears on the screen in filename, including prompts.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWcsu			   |
       +-----------------------------+-----------------------------+
       |CSI			     |Enabled			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       attributes(5)

WARNINGS

       script  can  pose  a  security risk when used in directories that are writable by other users (for example, /tmp), especially when run by a
       privileged user, that is, root. Be sure that typescript is not a link before running script.

SunOS 5.11							    30 Jan 2004 							 script(1)