Search, replace string in file1 with string from (lookup table) file2? Post: 302184488

Sponsored Content

Top Forums Shell Programming and Scripting Search, replace string in file1 with string from (lookup table) file2? Post 302184488 by gstuart on Friday 11th of April 2008 02:32:28 PM

04-11-2008

Registered User

This is absolutely wonderful! ... :-)

Here is my understanding of Franklin52's code:

Unix Manuals - AWK Reference

# == is �is equal�

tolower(string): Return the string with all upper case characters replaced with their lower case equivalents.

toupper(string): Return the string with all lower case characters replaced with their upper case equivalents.

FNR: Record number in input file.

NR: Number of records processed.

Thus, the above script translates (? - please correct me if I am mistaken) as

awk'
FNR==NR{a[tolower($1)]=$2;next}

while the record number (line) equals the total number of records (is true), do all of the following:
get $1 (the common gene name - converted to LOWERcase - required since the corresponding field in File_1 is lowercase; otherwise, it will fail to �match� - linux is case-sensitive) in the lookup file (File_2), set (change it) to the (already uppercase) systematic gene name ($2) in the same lookup table, then read the next record number (line);

tolower($1) in a{print "1 " a[tolower($1)] " tf " toupper($2)}

now, for each $1 in File_2 (now set to uppercase $2, from the lookup table), in the second file (File_1, the one to be converted), print
�1�, $2 from File_2; �tf�, $2 from File_1 (returned as uppercase, to convert the trailing lowercase c, w, -a, etc.)

' "File_2" "File_1"

File_1 = file to be processed (converted)
File_2 = �lookup file� ("common_to_systematic.tab)

?!

This works brilliantly!! Thank you so much, Franklin52!!

Have a super weekend! ... Greg :-)

gstuart

View Public Profile for gstuart

Find all posts by gstuart

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

string replacement using a lookup table

Dear all thanks for helping in advance.. Know this should be fairly simple but I failed in searching for an answer. I have a file (replacement table) containing two columns, e.g.: ACICJ ACIDIPHILIUM ACIF2 ACIDITHIOBACILLUS ACIF5 ACIDITHIOBACILLUS ACIC5 ACIDOBACTERIUM ACIC1 ACIDOTHERMUS...

2. Shell Programming and Scripting

Search & replace fields from file1 to file2

hi, I have two xml files with the name source.xml and tobe_replaced.xml. Sample data: source.xml contains: <?xml version="1.0"?> <product description="prod1" product_info="some/info"> <product description="prod2" product_info="xyz/allinfo"> <product description="abc/partialinfo"...

3. Shell Programming and Scripting

how to find string from file1 in file2

hi; i am looking for simple search script that find string from file1 in file 2 file 1 contain a loot of string like: 204080111111111 204080222222222 204080333333333 in each row and i would like to take the first row for example 204080111111111 from file1 and find it in file2 when it...

4. Shell Programming and Scripting

search from file1 and replace into file2

I have 2 files: file1.txt: 1|15|XXXXXX||9630716||0096000||30/04/2012|E|O|X||||20120525135617-30.04.2012|PAT66OLM|STA||||00001|STA_0096000_YYYPPPXTMEX00_20120525135617_02_P.pdf|...

5. Shell Programming and Scripting

How to retrieve a number or string from file1 and redirect into file2 in perl script?

hello forum members, I am siva ,As i am new to perl scripting i looking help from forum members. i need a sample program are command for pattern matching. I have file name infile1 which some data, I need to search the particular number are string in the file which repeats n number of...

6. UNIX for Dummies Questions & Answers

if matching strings in file1 and file2, add column from file1 to file2

I have very limited coding skills but I'm wondering if someone could help me with this. There are many threads about matching strings in two files, but I have no idea how to add a column from one file to another based on a matching string. I'm looking to match column1 in file1 to the number...

7. Shell Programming and Scripting

Match part of string in file2 based on column in file1

I have a file containing texts and indexes. I need the text between (and including ) INDEX and number "1" alone in line. I have managed this: awk '/INDEX/,/1$/{if (!/1$/)print}' file1.txt It works for all indexes. And then I have second file with years and indexes per year, one per line...

8. Shell Programming and Scripting

awk to search field2 in file2 using range of fields file1 and using match to another field in file1

I am trying to use awk to find all the $2 values in file2 which is ~30MB and tab-delimited, that are between $2 and $3 in file1 which is ~2GB and tab-delimited. I have just found out that I need to use $1 and $2 and $3 from file1 and $1 and $2of file2 must match $1 of file1 and be in the range...

9. Shell Programming and Scripting

Lookup value of file1 in file2 using a key

Trying to use awk to match each line in file1 with line in file2 using $1 and $2 and print. File2 is tab-delimeted as is the output and if there is no match then it is skipped. The awk below executes but the output is empty. I think file1 is being split on the : and being saved in array c which...

10. UNIX for Beginners Questions & Answers

Search partial string in a file and replace the string - UNIX

I have the below string which i need to compare with a file and replace this string in the file which matches closely. Can anyone help me on this. string(Scenario 1)- user::r--,user::ourfrd:r-- String(Scenario 2)- user::r-- File **** # file: /local/Desktop/myfile # owner: me # group:...

LEARN ABOUT BSD

isascii

CTYPE(3)						     Library Functions Manual							  CTYPE(3)

NAME

       isalpha,  isupper,  islower,  isdigit, isxdigit, isalnum, isspace, ispunct, isprint, isgraph, iscntrl, isascii, toupper, tolower, toascii -
       character classification macros

SYNOPSIS

       #include <ctype.h>

       isalpha(c)

       . . .

DESCRIPTION

       These macros classify ASCII-coded integer values by table lookup.  Each is a predicate returning nonzero for true, zero for false.  Isascii
       and  toascii  are defined on all integer values; the rest are defined only where isascii is true and on the single non-ASCII value EOF (see
       stdio(3S)).

       isalpha	      c is a letter

       isupper	      c is an upper case letter

       islower	      c is a lower case letter

       isdigit	      c is a digit

       isxdigit       c is a hex digit

       isalnum	      c is an alphanumeric character

       isspace	      c is a space, tab, carriage return, newline, vertical tab, or formfeed

       ispunct	      c is a punctuation character (neither control nor alphanumeric)

       isprint	      c is a printing character, code 040(8) (space) through 0176 (tilde)

       isgraph	      c is a printing character, similar to isprint except false for space.

       iscntrl	      c is a delete character(0177) or ordinary control character (less than 040).

       isascii	      c is an ASCII character, code less than 0200

       tolower	      c is converted to lower case.  Return value is undefined if not isupper(c).

       toupper	      c is converted to upper case.  Return value is undefined if not islower(c).

       toascii	      c is converted to be a valid ascii character.

SEE ALSO

       ascii(7)

7th Edition							   May 12, 1986 							  CTYPE(3)