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Top Forums Shell Programming and Scripting Search, replace string in file1 with string from (lookup table) file2? Post 302184384 by Franklin52 on Friday 11th of April 2008 10:08:12 AM
Old 04-11-2008
Quote:
Originally Posted by gstuart
Hello: I have another question. Please consider the following two sample, tab-delimited files:

File_1:

Abf1 YKL112w
Abf1 YAL054c
Abf1 YGL234w
Ace2 YKL150w
Ace2 YNL328c
Cup9 YDR441c
Cup9 YDR442w
Cup9 YEL040w
...


File 2:

...
ABF1 YKL112W
ACE2 YLR131C
CUP9 YPL177C
...

File_2 is a “lookup table;” I want to replace $1 in File_1 with the matching $2 field in File_2, additionally adding a middle column containing the string “tf”, and a column of “ones” (“1” in the first column position), all tab-delimited.

Additionally, it would be ideal if the case could be ignored for the search / replace, but that the alphabetical output be all uppercase [a-z] converted to [A-Z].

FYI, these are yeast genes; in addition to numbers and letters, some of the genes will contain dashes (e.g., YBR162W-A), but none will contain commas, semicolons, spaces, etc.

Output File_3:

1 YKL112W tf YKL112W
1 YKL112W tf YAL054C
1 YKL112W tf YGL234W
1 YLR131C tf YKL150W
1 YLR131C tf YNL328C
1 YLR131C tf YLR439W
1 YPL177C tf YDR441C
1 YPL177C tf YDR442W
1 YPL177C tf YEL040W
...
This should give the desired output:

Code:
 awk '
FNR==NR{a[tolower($1)]=$2;next} 
tolower($1) in a{print "1 " a[tolower($1)] " tf " toupper($2)}
' "File_2" "File_1"

Regards
 

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KICONV(3)						   BSD Library Functions Manual 						 KICONV(3)

NAME
kiconv_add_xlat16_cspair, kiconv_add_xlat16_cspairs, kiconv_add_xlat16_table -- kernel side iconv library LIBRARY
Kernel side iconv library (libkiconv, -lkiconv) SYNOPSIS
#include <sys/iconv.h> int kiconv_add_xlat16_cspair(const char *tocode, const char *fromcode, int flag); int kiconv_add_xlat16_cspairs(const char *foreigncode, const char *localcode); int kiconv_add_xlat16_table(const char *tocode, const char *fromcode, const void *data, int datalen); DESCRIPTION
The kiconv library provides multi-byte character conversion tables for kernel side iconv service. The kiconv_add_xlat16_cspair() function defines a conversion table using iconv(3) between fromcode charset and tocode charset. You can spec- ify flag to determine if tolower(3) / toupper(3) conversion is included in the table. The flag has following values. KICONV_LOWER KICONV_FROM_LOWER It generates a tolower table in addition to a character conversion table. The difference between two is tolower tocode or tolower fromcode. KICONV_UPPER KICONV_FROM_UPPER It generates a toupper table in addition to a character conversion table. The difference between two is toupper tocode or toupper fromcode. A tolower/toupper conversion is limited to single-byte characters. The kiconv_add_xlat16_cspairs() function defines two conversion tables which are from localcode to foreigncode and from foreigncode to localcode. These conversion tables also contain both tolower and toupper tables. The kiconv_add_xlat16_table() function defines a conversion table directly pointed by data whose length is datalen, not using iconv(3). SEE ALSO
iconv(3), tolower(3), toupper(3) BSD
July 17, 2003 BSD
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