Sponsored Content
Top Forums Shell Programming and Scripting extracting lines from a file1 which maches a pattern in file2 Post 302219415 by smriti_shridhar on Tuesday 29th of July 2008 03:28:33 AM
Old 07-29-2008
extracting lines from a file1 which maches a pattern in file2

Hi guys,
Can you help me in solving ths problem?
I have two files file1 and file2 as following:
===FILE1====
>LOC21
MASSKFCTVLSLALFLVLLTHANSAELFSFNFQTFNAANLILQGNASVSSSGQLRLTEVKSNGEPKVASL
VASFATAFTFNILAPILSNSADGLAFALVPVGSQPKFNGGFLGLFQNVTYDP
>LOC05
MASSKFSTVLSLALFLVLLTHANSAELFSFNFQTFNAANLILQGNASVSSSGQLRLTEVKSNGEPKVASL
GRAFYSAPIQIWDSTTGKVASFATAFTFNILAPILSNSADGLAFALVPVGSQPKFNGGFLGLFQNVTYDP
AKVLITYDSSTKLLVASLVYPSGS
>LOC48
MASLQTQMISFYAIFLSILLTTILFFKVNSTGEITSFSIPKFRPDQPNLIFQGGGYTTKEKLTLTKAVK

====FILE2====
LOC21
LOC48

I want to write the complete record form FILE1 (which starts from '>' sign) which matches the pattern in FILE2 into a new file FILE3 which shold look like -
>LOC21
MASSKFCTVLSLALFLVLLTHANSAELFSFNFQTFNAANLILQGNASVSSSGQLRLTEVKSNGEPKVASL
VASFATAFTFNILAPILSNSADGLAFALVPVGSQPKFNGGFLGLFQNVTYDP
>LOC48
MASLQTQMISFYAIFLSILLTTILFFKVNSTGEITSFSIPKFRPDQPNLIFQGGGYTTKEKLTLTKAVK


your help is highly appretiated Smilie

Thanks

Last edited by smriti_shridhar; 07-29-2008 at 04:30 AM.. Reason: to make it more informative
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

delete lines from file2 beginning w/file1

I've been searching around here and other places, but can't put this together... I've got a unique list of words in file 1 (one word on each line). I need to delete each line in file2 that begins with the word in file1. I started this way, but want to know how to use file1 words instead... (13 Replies)
Discussion started by: michieka
13 Replies

2. 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

3. UNIX for Dummies Questions & Answers

Extracting 482/300k columns no's with respective info. listed in file2 from file1

Hi, I have 2 files File 1: 1 2 3 4 5 6 .......etc until column 300K 1 23 21 24 12 22 1 23 21 24 12 22 1 23 21 24 12 22 1 23 21 24 12 22 1 23 21 24 12 22 1 23 21 24 12 22 1 23 21 24 12 22 . . etc until row 1411 File 2: (14 Replies)
Discussion started by: sogi
14 Replies

4. Shell Programming and Scripting

Display lines from file1 that are not in file2

Hi there, I know the command diff but what I want is slightly different. I have two files containing lines that look like md5sums. file1 5a1e8cee2eb2157c86e7266ee38e47c3 /tmp/file1 a254c48bdd064a40b82477b9fa5be05d /tmp/file2 2d57c72ec898acddf8a6bacb3f821572 /tmp/file3... (5 Replies)
Discussion started by: chebarbudo
5 Replies

5. Shell Programming and Scripting

Remove lines in file1 with values from file2

Hello, I have two data files: file1 12345 aa bbb cccc 98765 qq www uuuu 76543 pp rrr bbbbb 34567 nn ccc sssss 87654 qq ppp rrrrr file2 98765 34567 I need to remove the lines from file1 if the first field contains a value that appears in file2: output 12345 aa bbb cccc 76543 pp... (2 Replies)
Discussion started by: palex
2 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

Pattern Matching & replacing of content in file1 with file2

I have file 1 & file 2 with content mentioned below. I want to get the output as shown in file3. Requirement: check the content of column 1 & column 2, if value of column 1 in file1 matches with first column of file2 then remaining columns(2&3) of file2 should get replaced, also if value of... (4 Replies)
Discussion started by: siramitsharma
4 Replies

8. Shell Programming and Scripting

Looking for lines, which is present in file1 but not in file2 using UNIX and awk

I have 2 files with 7 fields and i want to print the lines which is present in file1 but not in file2 based on field1 and field2. Logic: I want to print all the lines, where there is a particular column1 and column2. And we do not find the set of column1 and column2 in file2. Example: "sc2/10... (3 Replies)
Discussion started by: NamS
3 Replies

9. Shell Programming and Scripting

Help with Shell Script to identify lines in file1 and write them to file2

Hi, I am running my pipeline and capturing all stout from multiple programs to a .txt file. I want to go into that .txt file and search for specific lines, and finally print those lines in a second .txt file. I can do this using grep, awk, or sed for each line, but have not been able to get... (2 Replies)
Discussion started by: hmortens
2 Replies

10. 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
TEST(1) 							   User Commands							   TEST(1)

NAME
test - check file types and compare values SYNOPSIS
test EXPRESSION test [ EXPRESSION ] [ ] [ OPTION DESCRIPTION
Exit with the status determined by EXPRESSION. --help display this help and exit --version output version information and exit An omitted EXPRESSION defaults to false. Otherwise, EXPRESSION is true or false and sets exit status. It is one of: ( EXPRESSION ) EXPRESSION is true ! EXPRESSION EXPRESSION is false EXPRESSION1 -a EXPRESSION2 both EXPRESSION1 and EXPRESSION2 are true EXPRESSION1 -o EXPRESSION2 either EXPRESSION1 or EXPRESSION2 is true -n STRING the length of STRING is nonzero STRING equivalent to -n STRING -z STRING the length of STRING is zero STRING1 = STRING2 the strings are equal STRING1 != STRING2 the strings are not equal INTEGER1 -eq INTEGER2 INTEGER1 is equal to INTEGER2 INTEGER1 -ge INTEGER2 INTEGER1 is greater than or equal to INTEGER2 INTEGER1 -gt INTEGER2 INTEGER1 is greater than INTEGER2 INTEGER1 -le INTEGER2 INTEGER1 is less than or equal to INTEGER2 INTEGER1 -lt INTEGER2 INTEGER1 is less than INTEGER2 INTEGER1 -ne INTEGER2 INTEGER1 is not equal to INTEGER2 FILE1 -ef FILE2 FILE1 and FILE2 have the same device and inode numbers FILE1 -nt FILE2 FILE1 is newer (modification date) than FILE2 FILE1 -ot FILE2 FILE1 is older than FILE2 -b FILE FILE exists and is block special -c FILE FILE exists and is character special -d FILE FILE exists and is a directory -e FILE FILE exists -f FILE FILE exists and is a regular file -g FILE FILE exists and is set-group-ID -G FILE FILE exists and is owned by the effective group ID -h FILE FILE exists and is a symbolic link (same as -L) -k FILE FILE exists and has its sticky bit set -L FILE FILE exists and is a symbolic link (same as -h) -O FILE FILE exists and is owned by the effective user ID -p FILE FILE exists and is a named pipe -r FILE FILE exists and read permission is granted -s FILE FILE exists and has a size greater than zero -S FILE FILE exists and is a socket -t FD file descriptor FD is opened on a terminal -u FILE FILE exists and its set-user-ID bit is set -w FILE FILE exists and write permission is granted -x FILE FILE exists and execute (or search) permission is granted Except for -h and -L, all FILE-related tests dereference symbolic links. Beware that parentheses need to be escaped (e.g., by backslashes) for shells. INTEGER may also be -l STRING, which evaluates to the length of STRING. NOTE: [ honors the --help and --version options, but test does not. test treats each of those as it treats any other nonempty STRING. NOTE: your shell may have its own version of test and/or [, which usually supersedes the version described here. Please refer to your shell's documentation for details about the options it supports. GNU coreutils online help: <http://www.gnu.org/software/coreutils/> Report test translation bugs to <http://translationproject.org/team/> AUTHOR
Written by Kevin Braunsdorf and Matthew Bradburn. COPYRIGHT
Copyright (C) 2013 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. SEE ALSO
The full documentation for test is maintained as a Texinfo manual. If the info and test programs are properly installed at your site, the command info coreutils 'test invocation' should give you access to the complete manual. GNU coreutils 8.22 June 2014 TEST(1)
All times are GMT -4. The time now is 12:04 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy