BTW, when you post sample data, please use data that can be used for testing and can produce proper results, cause I spent 5 minutes editing your sample "files" to match proper IPs and creating "srv2" and "srv3".
Hi All,
I have a string like below:
str="Hold=True Map=False 'This will map the data' Run=Yes Modify=False"
I want to print the field Run=Yes and retrive the value "Yes". I cannot use simple awk command because the position of the "Run" will be different at different times. Is there a way... (6 Replies)
I have about 20 CSV's that all look like this:
"","","","","","","","","","","","","","","",""What I've been told I need to produce is the exact same thing, but with each file now containing the start_code from every other file where the email matches.
It doesn't matter if any of the other... (1 Reply)
I have a flat file
test.log
red,5,,,,,
green,7,,,,,
blue,4,,,,,
red,8,,,,,
green,9,,,,,
How i get a a result:
blue,4,,,,,
green,16,,,,,
red,13,,,,,
Thanks
Video tutorial on how to use code tags in The UNIX and Linux Forums. (2 Replies)
Hello,
I have a file with such structure:
>ENSGALG00000000011|ENSGALT00000000012|57|1123|1125
AACTGTGTGTTTTTT
>ENSGALG00000000012|ENSGALT00000000013|57|1145|1155
AAAAAAGGTCCTGTGTGC
>ENSGALG00000000015|ENSGALT00000000014|57|1144|1155
AAAATGTGTGTGTGTGTGTGTG
I want to use another file... (8 Replies)
this is part of a KT i am going thru.
i am writing a script in bash shell, linux where i have 2 columns where 1st signifies the nth hour like 00, 01, 02...23 and 2nd the file size.
sample data attached.
Desired output is 3 columns which will give the nth hour, number of entries in nth hour and... (3 Replies)
Hello,
I am looking to output all of the lines from file2 whose 11th field is present in the first field in file1. Then the second field from file1 should be appended as such:
file1:
2222 0.35
4444 0.25
5555 0.75
file2:
col1 col2 col3 col4 col5 col6 col7 col8 col9 col10 1111
col1 col2... (4 Replies)
In the awk below I am trying to set/update the value of $14 in file2 in
bold, using the matching NM_ in $12 or $9 in file2
with the NM_ in $2 of file1.
The lengths of $9 and $12 can be variable but what is consistent is the start pattern
will always be NM_ and the end pattern is always ;... (2 Replies)
I apologize in advance, but I continue to have trouble searching for matches between two files and then printing portions of each to output in awk and would very much appreciate some help.
I have data as follows:
File1
PS012,002 PRQ 0 1 1 17 1 0 -1 3 2 1 2 -1 ... (7 Replies)
In the awk below I am trying to get the average of the sum of $7 if the string in $4 matches in the line below it. The --- in the desired out is not needed, it is just to illustrate the calculation. The awk executes and produces the current out. I am not sure why the middle line is skipped and the... (2 Replies)
Discussion started by: cmccabe
2 Replies
LEARN ABOUT DEBIAN
vcf-compare
VCF-COMPARE(1) User Commands VCF-COMPARE(1)NAME
vcf-compare - compare bgzipped and tabix indexed VCF files
SYNOPSIS
compare-vcf [OPTIONS] file1.vcf file2.vcf ...
DESCRIPTION
About: Compare bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix -p vcf file.vcf.gz)
OPTIONS -c, --chromosomes <list|file>
Same as -r, left for backward compatibility. Please do not use as it will be dropped in the future.
-d, --debug
Debugging information. Giving the option multiple times increases verbosity
-H, --cmp-haplotypes
Compare haplotypes, not only positions
-m, --name-mapping <list|file>
Use with -H when comparing files with differing column names. The argument to this options is a comma-separated list or one mapping
per line in a file. The names are colon separated and must appear in the same order as the files on the command line.
-R, --refseq <file>
Compare the actual sequence, not just positions. Use with -w to compare indels.
-r, --regions <list|file>
Process the given regions (comma-separated list or one region per line in a file).
-s, --samples <list>
Process only the listed samples. Excluding unwanted samples may increase performance considerably.
-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.
vcf-compare 0.1.5 July 2011 VCF-COMPARE(1)