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
file::mimeinfo::cookbook
File::MimeInfo::Cookbook(3pm) User Contributed Perl Documentation File::MimeInfo::Cookbook(3pm)NAME
File::MimeInfo::Cookbook - various code snippets
DESCRIPTION
Some code snippets for non-basic uses of the File::MimeInfo module:
Matching an extension
A file does not have to actually exist in order to get a mimetype for it. This means that the following will work:
my $extension = '*.txt';
my $mimetype = mimetype( $extension );
Mimetyping an scalar
If you want to find the mimetype of a scalar value you need magic mimetyping; after all a scalar doesn't have a filename or inode.
What you need to do is to use IO::Scalar :
use File::MimeInfo::Magic;
use IO::Scalar;
my $io_scalar = new IO::Scalar $data;
my $mimetype = mimetype( $io_scalar );
In fact most other "IO::" will work as long as they support the "seek()" and "read()" methods. Of course if you want really obscure
things to happen you can always write your own IO object and feed it in there.
Be aware that when using a filehandle like this you need to set the ":utf8" binmode yourself if apropriate.
Mimetyping a filehandle
Regrettably for non-seekable filehandles like STDIN simply using an "IO::" object will not work. You will need to buffer enough of the
data for a proper mimetyping. For example you could mimetype data from STDIN like this:
use File::MimeInfo::Magic;
use IO::Scalar;
my $data;
read(STDIN, $data, $File::MimeInfo::Magic::max_buffer);
my $io_scalar = new IO::Scalar $data;
my $mimetype = mimetype( $io_scalar );
Be aware that when using a filehandle like this you need to set the ":utf8" binmode yourself if apropriate.
Creating a new filename
Say you have a temporary file that you want to save with a more proper filename.
use File::MimeInfo::Magic qw#mimetype extensions#;
use File::Copy;
my $tmpfile = '/tmp/foo';
my $mimetype = mimetype($tmpfile);
my $extension = extensions($mimetype);
my $newfile = 'untitled1';
$newfile .= '.'.$extension if length $extension;
move($tmpfile, $newfile);
Force the use of a certain database directory
Normally you just need to add the dir where your mime database lives to either the XDG_DATA_HOME or XDG_DATA_DIRS environment variables
for it to be found. But in some rare cases you may want to by-pass this system all together. Try one of the following:
@File::MimeInfo::DIRS = ('/home/me/share/mime');
eval 'use File::MimeInfo';
die if $@;
or:
use File::MimeInfo;
@File::MimeInfo::DIRS = ('/home/me/share/mime');
File::MimeInfo->rehash();
This can also be used for switching between databases at run time while leaving other XDG configuration stuff alone.
AUTHOR
Jaap Karssenberg <pardus@cpan.org>
Copyright (c) 2005, 2012 Jaap G Karssenberg. All rights reserved. This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
SEE ALSO
File::MimeInfo
perl v5.14.2 2012-01-05 File::MimeInfo::Cookbook(3pm)