Could you please try to keep those both variables values into a single Input_file like as follows.
Also to get the above Input_file you could use paste var_file ref_file > Input_file
Then you could try to read their values by a loop and try to put your awkinside it.
Could you please try it out and let us know how it goes then. If you have more requirements in here, kindly post with full details on same.
Thanks,
R. Singh
Last edited by RavinderSingh13; 09-30-2016 at 04:47 PM..
This User Gave Thanks to RavinderSingh13 For This Post:
HI
I am trying to store the output of this awk command
awk -F, {(if NR==2) print $1} test.sr
in a variable when I am trying v= awk -F, {(if NR==2) print $1} test.sr
$v = awk -F, {(if NR==2) print $1} test.sr
but its not working out .
Any suggestions
Thanks
Arif (3 Replies)
Hi,
i have some files in one directory(say some sample dir) whose names will be like the following.
some_file1.txt
some_file2.txt.
i need to get the last modified file size based on file name pattern like some_
here i am able to get the value of the last modified file size using the... (5 Replies)
Hi folks,
I'm using bash and would like to do the following. I would like to read some values from the file and store it in the variable and use it.
My file is 1.txt and its contents are
VERSION=5.6
UPDATE=4
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i want to store the output of 'tail -5000 file' to a variable.
If i want to access the contents of that variable, it becomes kinda difficult because when the data is stored in the variable, everything is mushed together. you dont know where a line begins or ends.
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I am working on a script for Mac OS X that, among many other things, gets a list of all the installed Applications. I am pulling the list from the system_profiler command and formatting it using grep and awk. The problem is that I want to be able to use each result individually later in the script.... (3 Replies)
Hi,
My aim is to get the md5 hash of a file and store it in a variable.
var1="md5sum file1"
$var1
The above outputs fine but also contains the filename, so somthing like this 243ASsf25 file1
i just need to get the first part and put it into a variable.
var1="md5sum file1"... (5 Replies)
I'm working on a script in which gives certain details in its output depending on user-specified options. So, what I'd like to do is something like:
if
then
awkcmd='some_awk_command'
else
awkcmd='some_other_awk_command'
fi
Then, later in the script, we'd do something like:
... (5 Replies)
Hi All,
I was trying a shell script. I was unable to store file contents to a variable in the script. I have tried the below but unable to do it.
Input = `cat /path/op.diary`
Input = $(<op.diary)
I am using ksh shell. I want to store the 'op.diary' file contents to the variable 'Input'... (12 Replies)
Discussion started by: am24
12 Replies
LEARN ABOUT DEBIAN
vcf-isec
VCF-ISEC(1) User Commands VCF-ISEC(1)NAME
vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files
SYNOPSIS
vcf-isec [OPTIONS] file1.vcf file2.vcf ...
DESCRIPTION
About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files.
Note that lines from all files can be intermixed together on the output, which can yield unexpected results.
OPTIONS -C, --chromosomes <list|file>
Process the given chromosomes (comma-separated list or one chromosome per line in a file).
-c, --complement
Output positions present in the first file but missing from the other files.
-d, --debug
Debugging information
-f, --force
Continue even if the script complains about differing columns.
-o, --one-file-only
Print only entries from the left-most file. Without -o, all unique positions will be printed.
-n, --nfiles [+-=]<int>
Output positions present in this many (=), this many or more (+), or this many or fewer (-) files.
-p, --prefix <path>
If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)
-t, --tab <chr:pos:file>
Tab-delimited file with indexes of chromosome and position columns. (1-based indexes)
-w, --win <int>
In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a
SNP or an indel).
-h, -?, --help
This help message.
EXAMPLES
bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz
vcf-isec 0.1.5 July 2011 VCF-ISEC(1)