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Top Forums Shell Programming and Scripting Search avoiding special characters Post 302886263 by gina.lizar on Thursday 30th of January 2014 10:44:21 AM
Old 01-30-2014
Search avoiding special characters

Hi all,

I have a list which I want to search in another file.
I can do that using
grep -f

but the search is failing due to special characters, how do I solve this?

One row in that list is

Code:
amino-acid permease inda1 [Pyrenophora tritici-repentis  Pt-1C-BFP]gb|EDU41782.1| amino-acid permease inda1 [Pyrenophora  tritici-repentis Pt-1C-BFP]

Input file to be searched
Code:
comp1538736c0_seEON956710       5821833 putative amino-acid permease inda1 protein [Togninia minima UCRPA7]     1e-114  418     0       2       736     97      342     89.8%   80.1%
comp1538234c2_seEON956710       582.455 putative amino-acid permease inda1 protein [Togninia minima UCRPA7]     3e-18   96.7    2       2       229     338     413     71.1%   65.8%
comp1538600c3_seXP_001939063    5733127 amino-acid permease inda1 [Pyrenophora tritici-repentis Pt-1C-BFP]gb|EDU41782.1| amino-acid permease inda1 [Pyrenophora tritici-repentis Pt-1C-BFP]     5e-36   155     2       233     598     448 573      69.8%   59.5%

 

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fgrep(1)							   User Commands							  fgrep(1)

NAME
fgrep - search a file for a fixed-character string SYNOPSIS
/usr/bin/fgrep [-bchilnsvx] [-e pattern_list] [-f pattern-file] [pattern] [file...] /usr/xpg4/bin/fgrep [-bchilnsvx] [-e pattern_list] [-f pattern-file] [pattern] [file...] DESCRIPTION
The fgrep (fast grep) utility searches files for a character string and prints all lines that contain that string. fgrep is different from grep(1) and from egrep(1) because it searches for a string, instead of searching for a pattern that matches an expression. fgrep uses a fast and compact algorithm. The characters $, *, [, ^, |, (, ), and are interpreted literally by fgrep, that is, fgrep does not recognize full regular expressions as does egrep. These characters have special meaning to the shell. Therefore, to be safe, enclose the entire string within single quotes ('). If no files are specified, fgrep assumes standard input. Normally, each line that is found is copied to the standard output. The file name is printed before each line that is found if there is more than one input file. OPTIONS
The following options are supported: -b Precedes each line by the block number on which the line was found. This can be useful in locating block numbers by con- text. The first block is 0. -c Prints only a count of the lines that contain the pattern. -e pattern_list Searches for a string in pattern-list. This is useful when the string begins with a -. -f pattern-file Takes the list of patterns from pattern-file. -h Suppresses printing of files when searching multiple files. -i Ignores upper/lower case distinction during comparisons. -l Prints the names of files with matching lines once, separated by new-lines. Does not repeat the names of files when the pattern is found more than once. -n Precedes each line by its line number in the file. The first line is 1. -s Works silently, that is, displays nothing except error messages. This is useful for checking the error status. -v Prints all lines except those that contain the pattern. -x Prints only lines that are matched entirely. OPERANDS
The following operands are supported: file Specifies a path name of a file to be searched for the patterns. If no file operands are specified, the standard input will be used. /usr/bin/fgrep pattern Specifies a pattern to be used during the search for input. /usr/xpg4/bin/fgrep pattern Specifies one or more patterns to be used during the search for input. This operand is treated as if it were specified as -e pattern_list. USAGE
See largefile(5) for the description of the behavior of fgrep when encountering files greater than or equal to 2 Gbyte ( 2**31 bytes). ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of fgrep: LC_COLLATE, LC_CTYPE, LC_MES- SAGES, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 If any matches are found 1 If no matches are found 2 For syntax errors or inaccessible files, even if matches were found. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: /usr/bin/fgrep +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWcsu | +-----------------------------+-----------------------------+ /usr/xpg4/bin/fgrep +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWxcu4 | +-----------------------------+-----------------------------+ |CSI |Enabled | +-----------------------------+-----------------------------+ SEE ALSO
ed(1), egrep(1), grep(1), sed(1), sh(1), attributes(5), environ(5), largefile(5), XPG4(5) NOTES
Ideally, there should be only one grep command, but there is not a single algorithm that spans a wide enough range of space-time tradeoffs. Lines are limited only by the size of the available virtual memory. /usr/xpg4/bin/fgrep The /usr/xpg4/bin/fgrep utility is identical to /usr/xpg4/bin/grep -F (see grep(1)). Portable applications should use /usr/xpg4/bin/grep -F. SunOS 5.10 4 Oct 2002 fgrep(1)
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