So the portion in bold identifies ${id} as 1234 perfectly, however it does not store it so the for loop can use it and output the file with the 1234. Do I not need a loop even though ${id} could be multiple? Thank you .
Code:
# read id from target.txt
dir_path=C:/Users/cmccabe/Desktop/annovar
while IFS= read line
do
id=${line%.*}
echo "$dir_path/${id}.hg19_multianno.txt"
done < target.txt
# remove -dbnsfp33a fields 49-96 from multianno
${id}=(line)
for f in 'C:\Users\cmccabe\Desktop\annovar\${id}.txt.hg19_multianno.txt' ; do
bname=`basename $f`
pref=${bname%%$.*.txt}
awk -v F=49 -v T=96 '
BEGIN{FS=OFS="\t"}
{ b=T+1
t=T<NF?T:NF
for(i=F;i<NF-t+F;i++) $i=$(b++)
NF=--i}1' $f > C:/Users/cmccabe/Desktop/annovar/${pref}_dbremoved.txt
done
Last edited by cmccabe; 10-26-2017 at 10:04 AM..
Reason: added to scipt
I]hi all
i am in confusion since last 2 days :(
i posted thraed yesterday and some friends did help but still i couldnt get solution to my problem
let it be very clear
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to make some extraction . with the following input to get the right output.
input: /etc/exp/home/bin ====> output: exp
and
input: aex1234 ===> output: ex
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Following is input:
<P
align="justify"
><FONT size="+1" color="#221E1F">the tiny bundles of hairs that protrude from them. Waves in the fluid of the inner ear stimulate the hair cells. Like the rods and cones in the eye, the hair cells convert this physical stimulation into neural im<FONT... (1 Reply)
Hi,
I need to write a script, that will take the current date, time, and the output from # ps -eo pid,tid,class,rtprio,ni,pri,psr,pcpu,stat,wchan:14,comm
and spit it to a file, so it'll look like this...
PID TID CLS RTPRIO NI PRI PSR %CPU STAT WCHAN COMMAND
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Hello All,
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STPAGE020090930
xyzz aalc... (3 Replies)
Hi,
I have two files , one file with data file with attributes that need to be sent to another file to generate a predefined format.
Example:
File.txt
AP|{SSHA}VEEg42CNCghUnGhCVg==
APVG3|{SSHA}XK|"password"
AP3|{SSHA}XK|"This is test"
....
etc
---------
test.sh has... (1 Reply)
This is the sample input file
b 05/Jul/2010:07:00:10
a 05/Jul/2010:06:00:10
b 05/Jul/2010:07:00:10
c 05/Jul/2010:07:10:10
d 05/Jul/2010:08:00:10
e 05/Jul/2010:09:00:10
f 05/Jul/2010:10:00:10
h 05/Jul/2010:11:00:10
i 05/Jul/2010:12:00:10
j ... (9 Replies)
Dear All,
assume i have a file with content:
<Start>6000</Start>
<Stop>7599</Stop>
the output is:
6000
7000
7100
7200
7300
7400
7599
how should we use any awk, sed, perl can do this task, means to extract the uniq prefixes from the start and stop prefix.
Thanks
Jimmy (3 Replies)
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I am trying to use bash to loop through a directory /path/to/data using a prefix match from /path/to/file. That match is obtained and works using the code below (in green)... what I can not seem to do is populate or update the corresponding prefix_file.txt in /path/to/data with the values in each... (3 Replies)
Discussion started by: cmccabe
3 Replies
LEARN ABOUT DEBIAN
ecaccess-file-move
ECACCESS-FILE-MOVE(1p) User Contributed Perl Documentation ECACCESS-FILE-MOVE(1p)NAME
ecaccess-file-move - Move or Rename ECaccess Files
SYNOPSIS
ecaccess-file-move -version|-help|-manual
ecaccess-file-move [-debug] source-ecaccess-file target-ecaccess-file
DESCRIPTION
Allow moving an ECaccess File. When the move occurs within the same ECaccess File System then it is a rename. When the move occurs across
two different ECaccess File Systems then first a copy is done and then a delete of the original file is done (e.g. similar to ecaccess-
file-copy ... -erase).
The source-ecaccess-file and target-ecaccess-file are in the form [domain:][/user-id/]path. Please read the "Shell commands -> File
Management" section of the "ecaccess" guide for more information on the ECaccess File System.
ARGUMENTS
source-ecaccess-file
The source ECaccess File name.
target-ecaccess-file
The target ECaccess File name.
OPTIONS -version
Display version number and exits.
-help Print a brief help message and exits.
-manual Prints the manual page and exits.
-debug Display the SOAP messages exchanged.
EXAMPLES
ecaccess-file-move ec:test1.txt ec:test2.txt
Rename the test1.txt file in the ECFS directory of the authenticated user in test2.txt.
ecaccess-file-move ec:test1.txt home:test2.txt
Copy the test1.txt file from the ECFS directory of the authenticated user to the test2.txt file in the $HOME directory of the authenticated
user, then delete the test1.txt file from ECFS.
SEE ALSO
ecaccess-file-delete, ecaccess-file-get, ecaccess-file-mget, ecaccess-file-modtime, ecaccess-file-mput, ecaccess-file-rmdir, ecaccess-file-
copy, ecaccess-file-dir, ecaccess-file-mdelete, ecaccess-file-mkdir, ecaccess-file-chmod, ecaccess-file-put, ecaccess-file-size and
ecaccess.
perl v5.14.2 2012-04-16 ECACCESS-FILE-MOVE(1p)
10-26-2017
.