Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Awk- Indexing a list of numbers in file2 to print certain rows in file1
Top Forums Shell Programming and Scripting Awk- Indexing a list of numbers in file2 to print certain rows in file1 Post 303025330 by Geneanalyst on Tuesday 30th of October 2018 09:59:58 PM
Old 10-30-2018
Quote:
Originally Posted by vgersh99
something along these lines:
default 2 lines before/after
awk -f gene.awk file2.txt file1.txt
or 30 lines before/after
awk -v ba=30 -f gene.awk file2.txt file1.txt
where gene.awk is:
Code:
BEGIN {
  if(!ba) ba=2
}
FNR == NR {
   f2[$1];
   next
}
{
  f1all[FNR]=$0
  if ($3 in f2) {
    f1pat[$3]=FNR
    f1order[++order]=$3
  }
}
END {
  for (i=1;i<=order;i++)
    for(j=f1pat[f1order[i]]-ba;j<=f1pat[f1order[i]]+ba;j++)
      print f1all[j]
}

Or depending on your OS/version of grep you could do (for 2 lines before/after):
grep -A 2 -B 2 -F -f file2.txt file1.txt

Works great! Initially it was outputting 80 million rows, but that was my bad because a ".' had made its way into the column of data in file2
Last edited by Geneanalyst; 10-31-2018 at 07:18 AM..
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

replacing text in file1 with list from file2

I am trying to automate a process of searching through a set of files and replace all occurrences of a formatted text with the next item in the list of a second file. Basically i need to replace all instances of T????CLK???? with an IP address from a list in a second file. the second file is one IP... (9 Replies)
Discussion started by: dovetail
9 Replies

2. Shell Programming and Scripting

Find numbers from File1 within File2

Hi all, Please your help with this. I have 2 files, File_1-->contains a column of N numbers File_2-->contains many lines with other info and numbers from File_1 within it. I would like to get from File_2 all the lines containing within the same line each of N numbers from File_1... (4 Replies)
Discussion started by: cgkmal
4 Replies

3. UNIX for Advanced & Expert Users

print contents of file2 for matching pattern in file1 - AWK

File1 row is same as column 2 in file 2. Also file 2 will either start with A, B or C. And 3rd column in file 2 is always F2. When column 2 of file 2 matches file1 column, print all those rows into a separate file. Here is an example. file 1: 100 103 104 108 file 2: ... (6 Replies)
Discussion started by: i.scientist
6 Replies

4. 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

5. Shell Programming and Scripting

Search within file1 numbers from list in file2

Hello to all, I hope somebody could help me with this: I have this File1 (real has 5 million of lines): Number Category --------------- -------------------------------------- 8734060355 3 8734060356 ... (6 Replies)
Discussion started by: Ophiuchus
6 Replies

6. Shell Programming and Scripting

awk read in file1, gsub in file2, print to file3

I'm trying to use awk to do the following. I have file1 with many lines, each containing 5 fields describing an individual set. I have file2 which is a template config file with variable space holders to be replaced by the values in file1. I would like to substitute each set of values in file1 with... (6 Replies)
Discussion started by: msmehaffey
6 Replies

7. Shell Programming and Scripting

Print sequences from file2 based on match to, AND in same order as, file1

I have a list of IDs in file1 and a list of sequences in file2. I can print sequences from file2, but I'm asking for help in printing the sequences in the same order as the IDs appear in file1. file1: EN_comp12952_c0_seq3:367-1668 ES_comp17168_c1_seq6:1-864 EN_comp13395_c3_seq14:231-1088... (5 Replies)
Discussion started by: pathunkathunk
5 Replies

8. Shell Programming and Scripting

Remove rows from file2 if it exists in file1

I have 2 file, file1 and file2. file1 has some keys and file2 has keys+some other data. I want to remove the lines from file2,if the key for that line exists in file1. file1: key1 key2 flie2: key1,moredata key2,moredata key3,moredata Required output: key3,moredata Thanks EDIT:... (6 Replies)
Discussion started by: chacko193
6 Replies

9. UNIX for Dummies Questions & Answers

Compare file1 and file2, print matching lines in same order as file1

I want to print only the lines in file2 that match file1, in the same order as they appear in file 1 file1 file2 desired output: I'm getting the lines to match awk 'FNR==NR {a++}; FNR!=NR && a' file1 file2 but they are in sorted order, which is not what I want: Can anyone... (4 Replies)
Discussion started by: pathunkathunk
4 Replies

10. 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

LEARN ABOUT SUNOS

comm

comm(1) 							   User Commands							   comm(1)

NAME

       comm - select or reject lines common to two files

SYNOPSIS

       comm [-123] file1 file2

DESCRIPTION

       The comm utility reads file1 and file2, which must be ordered in the current collating sequence, and produces three text columns as output:
       lines only in file1; lines only in file2; and lines in both files.

       If the input files were ordered according to the collating sequence of the current locale, the lines  written  will  be	in  the  collating
       sequence of the original lines. If not, the results are unspecified.

OPTIONS

       The following options are supported:

       -1	Suppresses the output column of lines unique to file1.

       -2	Suppresses the output column of lines unique to file2.

       -3	Suppresses the output column of lines duplicated in file1 and file2.

OPERANDS

       The following operands are supported:

       file1	A path name of the first file to be compared. If file1 is -, the standard input is used.

       file2	A path name of the second file to be compared. If file2 is -, the standard input is used.

USAGE

       See largefile(5) for the description of the behavior of comm when encountering files greater than or equal to 2 Gbyte ( 2**31 bytes).

EXAMPLES

       Example 1: Printing a list of utilities specified by files

       If file1, file2, and file3 each contain a sorted list of utilities, the command

       example% comm -23 file1 file2  | comm -23 - file3

       prints a list of utilities in file1 not specified by either of the other files. The entry:

       example% comm -12 file1 file2 | comm -12 - file3

       prints a list of utilities specified by all three files. And the entry:

       example% comm -12  file2 file3 | comm -23 -file1

       prints a list of utilities specified by both file2 and file3, but not specified in file1.

ENVIRONMENT VARIABLES

       See  environ(5)	for  descriptions  of  the  following  environment  variables that affect the execution of comm: LANG, LC_ALL, LC_COLLATE,
       LC_CTYPE, LC_MESSAGES, and NLSPATH.

EXIT STATUS

       The following exit values are returned:

       0	All input files were successfully output as specified.

       >0	An error occurred.

ATTRIBUTES

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

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWesu			   |
       +-----------------------------+-----------------------------+
       |CSI			     |enabled			   |
       +-----------------------------+-----------------------------+
       |Interface Stability	     |Standard			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       cmp(1), diff(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5)

SunOS 5.10							    3 Mar 2004								   comm(1)
All times are GMT -4. The time now is 06:44 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy