I would like to remove characters from column 7 so that from an input file looking like this:
>HWI-EAS422_12:4:1:69:89 GGTTTAAATATTGCACAAAAGGTATAGAGCGT U0 1 0 0 ref_chr8.fa 6527777 F DD
I get something like that in an output file:
... (13 Replies)
Hi all,
I'm new to Unix and work primarily in bioinformatics. I am in need of a script which will allow me to replace "1" with "chr1" in only the first column of a file which looks like such:
1 10327 rs112750067 T C . PASS ASP;RSPOS=10327;... (4 Replies)
I have a file which looks like this:
73450 articles and news developmental psychology 2006-03-30 16:22:40 1 http://www.usnews.com
73450 articles and news developmental psychology 2006-03-30 16:22:40 2 http://www.apa.org
73450 articles and news developmental psychology 2006-03-30... (1 Reply)
I have a file having the following entries:
test1 test2 test3
11 22 33
22 44 66
99 99 44
---
I want to add a column so that the above file becomes:
test1 test2 test3 notest
11 22 33 *
22 44 66 *
99 99 44 *
---
Thanks (6 Replies)
Hello,
I have this sentence :Pattern1 Pattern2 Pattern3 Pattern4-which-contains-HELLO-string-and-other-stuff-and-second-HELLO-and-third-HELLO
I want to delete everything between the 3rd tab (\t) and the FIRST pattern "HELLO" of the line.
Result expected is : Pattern1 ... (7 Replies)
Hi,
Can anyone please tell me about how we can delete an entire column from a tab delimited file?
Mu input_file.txt looks like this:
And I want the output as:
I used the below code
nawk -v d="1" 'BEGIN{FS=OFS="\t"}{$d=""}{print}' input_file.txtBut in the output, the first column is... (5 Replies)
I have tried the following to no avail.
xargs -n8 < test.txt
awk '{if(NR%6!=0){p=""}else{p="\n"};printf $0" "p}' Mod_Alm_log.txt > test.txt
I have tried different variations of the above, the problem is mixes lines together.
And it includes the tags "%a and %A" I need them to be all tab... (16 Replies)
input
"A","B","C,D","E","F"
"S","T","U,V","W","X"
"AA","BB","CC,DD","EEEE","FFF"
required output:
"A","B","C,D","C,D","F"
"S", T","U,V","U,V","X"
"AA","BB","CC,DD","CC,DD","FFF"
tried using awk but double quotes not preserving for every field. any help to solve this is much... (5 Replies)
Hello Everyone..
I want to replace the retail col from FileI with cstp1 col from FileP if the strpno matches in both files
FileP.txt
... (2 Replies)
Discussion started by: YogeshG
2 Replies
LEARN ABOUT DEBIAN
text::trim
Text::Trim(3pm) User Contributed Perl Documentation Text::Trim(3pm)NAME
Text::Trim - remove leading and/or trailing whitespace from strings
VERSION
version 1.02
SYNOPSIS
use Text::Trim;
$text = " important data
";
$data = trim $text;
# now $data contains "important data" and $text is unchanged
# or:
trim $text; # work in-place, $text now contains "important data"
@lines = <STDIN>;
rtrim @lines; # remove trailing whitespace from all lines
# Alternatively:
@lines = rtrim <STDIN>;
# Or even:
while (<STDIN>) {
trim; # Change $_ in place
# ...
}
DESCRIPTION
This module provides functions for removing leading and/or trailing whitespace from strings. It is basically a wrapper around some simple
regexes with a flexible context-based interface.
EXPORTS
All functions are exported by default.
CONTEXT HANDLING
void context
Functions called in void context change their arguments in-place
trim(@strings); # All strings in @strings are trimmed in-place
ltrim($text); # remove leading whitespace on $text
rtrim; # remove trailing whitespace on $_
No changes are made to arguments in non-void contexts.
list context
Values passed in are changed and returned without affecting the originals.
@result = trim(@strings); # @strings is unchanged
@result = rtrim; # @result contains rtrimmed $_
($result) = ltrim(@strings); # like $result = ltrim($strings[0]);
scalar context
As list context but multiple arguments are stringified before being returned. Single arguments are unaffected. This means that under
these circumstances, the value of $" ($LIST_SEPARATOR) is used to join the values. If you don't want this, make sure you only use single
arguments when calling in scalar context.
@strings = (" hello
", " there
");
$trimmed = trim(@strings);
# $trimmed = "hello there"
local $" = ', ';
$trimmed = trim(@strings);
# Now $trimmed = "hello, there"
$trimmed = rtrim;
# $trimmed = $_ minus trailing whitespace
Undefined values
If any of the functions are called with undefined values, the behaviour is in general to pass them through unchanged. When stringifying a
list (calling in scalar context with multiple arguments) undefined elements are excluded, but if all elements are undefined then the return
value is also undefined.
$foo = trim(undef); # $foo is undefined
$foo = trim(undef, undef); # $foo is undefined
@foo = trim(undef, undef); # @foo contains 2 undefined values
trim(@foo) # @foo still contains 2 undefined values
$foo = trim('', undef); # $foo is ''
FUNCTIONS
trim
Removes leading and trailing whitespace from all arguments, or $_ if none are provided.
rtrim
Like trim() but removes only trailing (right) whitespace.
ltrim
Like trim() but removes only leading (left) whitespace.
UNICODE
Because this module is implemented using perl regular expressions, it is capable of recognising and removing unicode whitespace characters
(such as non-breaking spaces) from scalars with the utf8 flag on. See Encode for details about the utf8 flag.
Note that this only applies in the case of perl versions after 5.8.0 or so.
SEE ALSO
Brent B. Powers' String::Strip performs a similar function in XS.
AUTHOR
Matt Lawrence <mattlaw@cpan.org>
ACKNOWLEDGEMENTS
Terrence Brannon <metaperl@gmail.com> for bringing my attention to String::Strip and suggesting documentation changes.
perl v5.10.1 2010-06-07 Text::Trim(3pm)