In awk, NR is the total input lines seen, while FNR is the number of input lines seen in the current file. So this essentially means: if we're processing the first file, "do this" (the code in the first set of braces {...}).
That code sets an associate array to the value of the 2nd column (in the first file, remember), where the index is the 1st column -- which is common in both files.
Now do a "next" which means do not process any more code for the current line. This ensures the rest of the awk script is not executed for the first file.
So the first "pattern/program" applies to the first file -- and only the first -- while the second "pattern/program" applies to the second (and subsequent) file(s).
The second pattern/program looks at each line (in the second file) and if the first column is found in the array A, and if the value is not null or not blank, it runs the portion between the braces.
The code in the braces simply replaces the 5th field of that line with the contents of what was seen in line indexed by the first column in the first file.
Hi guys I want to print the values by using this script but its giving the no of rows and columns as input instead of values
Would you plz help me on this
FILE- chr1.txt
1981 1
1971 1
1961 1
1941 1
perl script
#!/usr/bin/perl -w
$infile1 = 'chr1.txt';
$outfile3 = 'out3.txt';
... (3 Replies)
I have read another post about this issue and am wondering how to adapt it
to my own, much simpler, issue.
I have a file of user IDs like so:
333333
321321
546465
...etc
I need to take each number and use it to print records wherein the 5th
field matches the user ID pulled from the... (2 Replies)
Hi, Guys. Please help me to find solution to this problem using shell scripting.
I have an INPUT file with 4 columns separated by tab. Each block of records is separated by -----
-----
Sample1 5402 6680 Pattern01
Sample2 2216 2368 Pattern02... (6 Replies)
Hi everyone,
I have file1 and file2 comma separated both.
file1 is:
Header1,Header2,Header3,Header4,Header5,Header6,Header7,Header8,Header9,Header10
Code7,,,,,,,,,
Code5,,,,,,,,,
Code3,,,,,,,,,
Code9,,,,,,,,,
Code2,,,,,,,,,file2... (17 Replies)
Hello Friends,
I have a CDR file and i need to print out 2 columns with their field position which matches to some constant values,
a part of input file
CZ=1|CZA=1|DIAL=415483420001|EE=13|ESF=1|ET=|FF=0|9|MNC=99|MNP=9041|MTC=0|NID=2|NOA=international|ON=1|
OutPut
... (3 Replies)
Hi Experts,
I am trying to get the output from a matching pattern but unable to construct the awk command:
file :
aa bb cc 11
dd aa cc 33
cc 22 45 68
aa 33 44 44
dd aa cc 37
aa 33 44 67
I want the output to be : ( if $1 match to "aa" start of the line,then print $4 of that line, and... (3 Replies)
Hello,
I have two files file 1 and file 2 each having result of a query on certain database tables and need to compare for Col1 in file1 with Col3 in file2, compare Col2 with Col4 and output the value of Col1 from File1 which is a) not present in Col3 of File2 b) value of Col2 is different from... (2 Replies)
I want to print only the lines in file2 that match file1, in the same order as they appear in file 1
file1
file2
desired output:
I'm getting the lines to match
awk 'FNR==NR {a++}; FNR!=NR && a' file1 file2
but they are in sorted order, which is not what I want:
Can anyone... (4 Replies)
I would like to compare values in column 8, and grep the ones where the different is > 1, columns 1 and 2 are the key for array.
Every 4 rows the records values in columns 1 and 2 changed. Then, the comparison in the column 8 need to be done for the 4 rows everytime columns 1 and 2 changed
... (4 Replies)
Discussion started by: jiam912
4 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)
05-17-2012
