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