Sponsored Content
Top Forums Shell Programming and Scripting Search, replace string in file1 with string from (lookup table) file2? Post 302184136 by gstuart on Thursday 10th of April 2008 03:24:50 PM
Old 04-10-2008
Search, replace string in file1 with string from (lookup table) file2?

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 is related to (but different from) my earlier query,

https://www.unix.com/shell-programmin...#post302183287

Here, the first column is a “dummy” weight value, to maintain “field compatibility,” with my earlier file, as shown in this example:

1 a gi b
1 a pp a
1 a pp c
1 t gi u
1 t gi w
1 t gi x
1 t pp z
2 a pp d
2 a pp e
2 t gi v
2 t gi z
3 a pp b
3 t gi y
...

Ultimately, I will end up with a file like this, with $1 = weight, $2 = gene1, $3 = association, $4 = gene2:


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
...
1 YBL012C gi YCL045C
1 YBL012C pp YBL012C
5 YBL012C pp YHR039C-A
1 YLR363W-A gi YNL143C
4 YLR363W-A gi YPR123C
1 YLR363W-A gi YLR467W
1 YLR363W-A pp YNR073C
2 YBL012C pp YGL232W
2 YBL012C pp YOR102W
2 YLR363W-A gi YFL066C
2 YLR363W-A gi YNR073C
3 YBL012C pp YCL045C
3 YLR363W-A gi YKL100C
...

Thank you - Once again, *very* much appreciated!

Sincerely, Greg S. :-)
 

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... (10 Replies)
Discussion started by: roussine
10 Replies

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"... (2 Replies)
Discussion started by: dragon.1431
2 Replies

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... (1 Reply)
Discussion started by: kpinto
1 Replies

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|... (2 Replies)
Discussion started by: pparthiv
2 Replies

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... (0 Replies)
Discussion started by: workforsiva
0 Replies

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... (3 Replies)
Discussion started by: pathunkathunk
3 Replies

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... (3 Replies)
Discussion started by: phoebus
3 Replies

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... (6 Replies)
Discussion started by: cmccabe
6 Replies

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... (3 Replies)
Discussion started by: cmccabe
3 Replies

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:... (6 Replies)
Discussion started by: sarathy_a35
6 Replies
expand(1)						      General Commands Manual							 expand(1)

NAME
expand, unexpand - Replaces tab characters with spaces or spaces with tab characters SYNOPSIS
Current syntax expand [-t tablist] [file...] unexpand [-a | -t tablist] [file...] Obsolescent syntax expand [-tabstop | -tab1,tab2,...,tabn] [file...] STANDARDS
Interfaces documented on this reference page conform to industry standards as follows: expand: XCU5.0 unexpand: XCU5.0 Refer to the standards(5) reference page for more information about industry standards and associated tags. OPTIONS
Replaces spaces at the beginning of each line with a tab, and inserts tab characters wherever their presence compresses the resultant file by replacing two or more characters. When the -t option is specified with the unexpand command, the -a option has no effect. (This option applies to the unexpand command only.) Specifies the tab stops. The tablist argument consists of a single positive decimal integer or multiple positive decimal integers, separated by spaces or commas, in ascending order. If a single number is specified, tabs are set tab- list column positions apart instead of the default (8). If multiple numbers are specified, tabs are set at those specific column posi- tions. Tabbing to tab stop position n thus causes the next character output to be in the (n+1)th column position on that line. If expand has to process a tab character at a position beyond the last of those specified in a multiple tab stop list, the tab char- acter is replaced by a single space in the output. Sets tab stops tabstop spaces apart instead of the default (8). (Obsolescent) Sets tab stops at specified columns. (Obsolescent) [Tru64 UNIX] Columns are measured in bytes. OPERANDS
The path name of a file to be processed. If you do not specify this operand, standard input is read. DESCRIPTION
The expand command changes tab characters to spaces in the named files, or the standard input, and writes the result to the standard out- put. The unexpand command puts tab characters into the data from the standard input, or the named files, and writes the result to the standard output. Backspace characters are preserved in the output and decrement the column count for tab calculations. The column position count cannot be decremented below one. The expand command is useful for preprocessing character files (before sorting, looking at specific columns, and so on.) that contain tab characters. By default, unexpand converts only spaces that are within sequences of spaces and tab characters at the beginnings of lines. Use -a to convert other sequences of spaces. NOTES
If the expand command encounters difficulties opening any specified file, it writes an error message to standard error and terminates imme- diately with an error status. If the unexpand command encounters difficulties opening any specified file, it writes an error message to standard error and continues operation. The exit status will reflect the error. EXIT STATUS
The following exit values are returned by either command: Successful completion. An error occurred. EXAMPLES
To replace tab characters in file with spaces, enter: expand file To replace the spaces in file with tab characters, enter: unexpand -a file ENVIRONMENT VARIABLES
The following environment variables affect the execution of expand and unexpand: Provides a default value for the internationalization variables that are unset or null. If LANG is unset or null, the corresponding value from the default locale is used. If any of the inter- nationalization variables contain an invalid setting, the utility behaves as if none of the variables had been defined. If set to a non- empty string value, overrides the values of all the other internationalization variables. Determines the locale for the interpretation of sequences of bytes of text data as characters (for example, single-byte as opposed to multibyte characters in arguments). Determines the locale for the format and contents of diagnostic messages written to standard error. Determines the location of message catalogues for the processing of LC_MESSAGES. SEE ALSO
Commands: fold(1), tabs(1) Standards: standards(5) expand(1)
All times are GMT -4. The time now is 09:32 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy