I have ~100 text files in a directory that I am trying to parse and output to a new file. I am looking for the words chr,start,stop,ref,alt in each of the files. Those fields should appear somewhere in those files. The first two fields of each new set of rows is also printed. Since this is on a windows os I used "path\to\folder' in the bash
example of files to search (each is a seperate file)
Code:
name1 1111 chr start stop ref alt comment
1 10 25 a t snp
1 20 75 t - del
2 30 120 - a ins
10 10 80 a g snpname2 222 id chr start stop ref alt comment
1111 1 10 25 a g snpname3 333333 id symbol chr start stop ref alt comment
222 name 1 20 75 c - del
222 name 2 30 120 - t ins
desired output
Code:
name1 1111 chr start stop ref alt
1 10 25 a t
1 20 75 t -
2 30 120 - a
10 10 80 a gname2 222 chr start stop ref alt
1 10 25 a gname3 333333 chr start stop ref alt
1 20 75 c -
2 30 120 - t
Thank you .
bash tried
Code:
for f in "C:\Users/test\Desktop\file\folder*.txt" ; do
bname=${f##*/}
pref=${bname%%.bam}
awk "/chr/{found=1}/start/{if(found)/stop/{if(found)/ref/{if(found)/alt/{if(found) $f print > ${pref}_edit.txt
done
I wanted to search in all the sub directories under /vob/project (recurse) in everything inside /vob/project.
search.run
for x in `cat search.strings`
do
find /vob/project -type f -print | xargs grep -i $x > ~/$x.txt
done
search.string
hello
whoami
I am getting the error ... (5 Replies)
Hi,
I have a file which contains the following :
select * from test where test_id=1;
select id
from test1, test2 where test_id=1 and test_id=2;
select * from
test1, test2, test3 where test_id=4 and test2_id where in (select test2_id from test2);
select
id1, id2 from test ... (6 Replies)
Hi all,
I am looking for a coomand to search for the keywords in susequenct lines. Keyword1 in a line and Keyword2 in the very next line.
Once i found the combination ineed to print the lines with patterns and the line above and one below.
I am giving an example here: Keywords are :ERROR and... (12 Replies)
Hi all,
how to recursively search for a list of keywords in a given directory??
for example:
suppose i have kept all the keywords in a file called "procnamelist" (in separate line)
and i have to search recursively in a directory called "target/dir"
if i am not doing recursive search then... (4 Replies)
I have a huge list of files in an Unix directory (around 10000 files).
I need to be able to search for a certain keyword only within files that are modified between certain date and time, say for e.g 2012-08-20 12:30 to 2012-08-20 12:40
Can someone let me know what would be the fastest way... (10 Replies)
have a very big file where need to format it like below
example file:
abcd today
is
great
day;
search keyword 'abcd' and append to it all words till we reach ; to make it a single line.
output should look like.
abcd today is great day;
There are many occurrence of such... (2 Replies)
Hi ,
I have been trying to write a perl script to do this job. But i am not able to achieve the desired result. Below is my code.
my $current_value=12345;
my @users=("bob","ben","tom","harry");
open DBLIST,"<","/var/tmp/DBinfo";
my @input = <DBLIST>;
foreach (@users)
{
my... (11 Replies)
Hi Team,
i have a web ui where user will be passing values and the output will be saved to a file say test with the following contents .
These below mentioned values will change according to the user_input
Just gave here one example
Contents of file test is given below
Gateway... (7 Replies)
Discussion started by: venkitesh
7 Replies
LEARN ABOUT DEBIAN
dpkg-www
DPKG-WWW(1) General Commands Manual DPKG-WWW(1)NAME
dpkg-www - program to remotely open a WWW Debian package browser
SYNOPSIS
dpkg-www [-s|--stdout] [-h|--host host] [query]
DESCRIPTION
dpkg-www is used to remotely control a WEB browser and open a dpkg URL on the local host from an interactive shell or script.
If the command is invoked while running under X-window the script will try to find an installed X browser to open the specified URL. If
not running under X it will try to use a text browser instead.
If Netscape is found and a Netscape instance is already running it will be asked to open the dpkg URL on localhost with the optional query
supplied on the command line. If there is no browser running, it will start automatically a new one.
The functionality provided by this program is identical to running a web browser with the -remote openURL(http://localhost/cgi-bin/dpkg)
argument or opening the same URL from within the browser.
dpkg-www-installer is an helper application which can configured in the WWW browser for web installation. It should never be invoked
directly by the user.
OPTIONS -s, --stdout
Redirect output to stdout. Requires one of the text browsers (lynx, lynx-ssl or links) installed.
-h, --host host
Send the query to a remote host, where dpkg-www must be installed.
query Specifies an optional package name, an absolute pathname or a query argument which is passed to the dpkg cgi-bin. See dpkg-www(8)
for more information about the use of the cgi.
FILES
/etc/dpkg-www.conf
~/.dpkg-www
Configuration files for dpkg-www. It is not necessary for these files to exist, there are sensible defaults for everything, but you
can specify your preferred www browser with the DPKG_WWW_BROWSER variable, for example: DPKG_WWW_BROWSER=mozilla
EXAMPLES
dpkg-www
This would open a dpkg URL on localhost listing all the installed packages.
dpkg-www bash
This would open a dpkg URL asking info on the bash package.
dpkg-www -h pisolo bash
This would open a dpkg URL asking info on the bash package on host pisolo.
dpkg-www 'dpkg*'
This would open a dpkg URL listing all packages matching dpkg*.
dpkg-www /bin/bash
This would open a dpkg URL asking info on the package(s) owning the file /bin/bash .
dpkg-www depends=svgalib
This would open a dpkg URL listing all packages depending on svgalib.
dpkg-www --stdout depends=awk | grep ^ii
This would list on stdout all packages depending on awk and grep all lines of installed packages.
SEE ALSO dpkg(8), dpkg-www(8)AUTHOR
Massimo Dal Zotto <dz@debian.org>.
Bugs should be reported via the normal Debian bug reporting system.
LICENCE
dpkg-www is licensed under the GNU General Public License version 2.
September 1, 2004 DPKG-WWW(1)
01-11-2016
.