Search, replace string in file1 with string from (lookup table) file2? Post: 302184136

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

04-10-2008

Registered User

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. :-)

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 HPUX

merge

merge(1)						      General Commands Manual							  merge(1)

NAME

       merge - three-way file merge

SYNOPSIS

       file1 file2 file3

DESCRIPTION

       combines  two  files  that are revisions of a single original file.  The original file is file2, and the revised files are file1 and file3.
       identifies all changes that lead from file2 to file3 and from file2 to file1, then deposits the merged text into file1.	If the	option	is
       used, the result goes to standard output instead of file1.

       An  overlap  occurs  if both file1 and file3 have changes in the same place.  prints how many overlaps occurred, and includes both alterna-
       tives in the result.  The alternatives are delimited as follows:

	      lines in file1
	      lines in file3

       If there are overlaps, edit the result in file1 and delete one of the alternatives.

       This command is particularly useful for revision control, especially if file1 and file3 are the ends of two branches that have file2  as  a
       common ancestor.

EXAMPLES

       A typical use for is as follows:

	      1.   To  merge  an  RCS branch into the trunk, first check out the three different versions from RCS (see co(1)) and rename them for
		   their revision numbers: 5.2, 5.11, and 5.2.3.3.  File 5.2.3.3 is the end of an RCS branch that split off the trunk at file 5.2.

	      2.   For this example, assume file 5.11 is the latest version on the trunk, and is also a revision  of  the  "original"  file,  5.2.
		   Merge the branch into the trunk with the command:

	      3.   File  5.11  now  contains  all  changes  made on the branch and the trunk, and has markings in the file to show all overlapping
		   changes.

	      4.   Edit file 5.11 to correct the overlaps, then use the command to check the file back in (see ci(1)).

WARNINGS

       uses the ed(1) system editor.  Therefore, the file size limits of ed(1) apply to

AUTHOR

       was developed by Walter F. Tichy.

SEE ALSO

       diff3(1), diff(1), rcsmerge(1), co(1).

																	  merge(1)