Works only if the second file has a space as field separator as in the provided example, but who knows?
Yes Franklin52, thats true. but I thought it would be better if we do not use substr($0,2,6) since we really do not know how many char ? whether its of fixed length or not in real data.
---edit---
OR this could be an alternative if space separated
Code:
$ awk 'FNR==NR{A[$1];next}substr($1,2) in A' file1 file2
Last edited by Akshay Hegde; 12-13-2013 at 03:52 PM..
This User Gave Thanks to Akshay Hegde For This Post:
hello
I want to do a pattern match for string in the if statement, but I am not sure how to use regex inside the if statement.
I am looking for something like this:
if {2,3} ]; then
.....
....
...
fi (7 Replies)
I have a file with the following format
12g data/datasets/cct 8g data/dataset/cct
10 g data/two 5g data/something_different
10g something_different
5g data/two
is there a way to loop through this... (1 Reply)
Good Morning,
I was wondering if anybody could tell me how to achieve the following, preferably with a little commenting for understanding.
I have 2 files, each with multiple rows with multiple columns.
I need to find each row where the value in column 1 of file 1 matches column 1... (10 Replies)
Hello,
Here I have some grep command which is not working correctly:
cat file1.txt:
apples
Date: Sun, 24 Feb 2013 8:14:06 -0800
peaches melons
cherry sky cloud
green purple
yellow
cat file2.txt:
apples
Date
peaches melons 0800
cherry sky cloud
green purple
black (2 Replies)
Hi
I have a problem where I have a large amount of files that I need to scan and return a line and its following line, but only when the following line begins with a string.
String one - line one must begin with 'Bill'
String two - line two must begin with 'Jones'.
If these two... (7 Replies)
Hi
I will appreciate it if you can help me out. I have a file that contains this data
System Load: 3244 card: 1903 CPU: 6% card: 1904 CPU: 6% card: 1905 CPU: 28% card: 1906 CPU: 28% card: 1907 CPU: 36% card: 1908 CPU: 37%
I need to manipulate and output this as
system_load:3244... (2 Replies)
Hello Everyone ,
Iam a newbie to shell programming and iam reaching out if anyone can help in this :-
I have two files
1) Insert.txt
2) partition_list.txt
insert.txt looks like this :-
insert into emp1 partition (partition_name)
(a1,
b2,
c4,
s6,
d8)
select
a1,
b2,
c4, (2 Replies)
I have two files and desire to use the strings from $1 of file 1 (file1.txt) as search criteria to find matches in $2 of file 2 (file2.txt). If matches are found I want to output the entire line of file 2 (file2.txt) followed by fields $2-$11 of file 1 (file1.txt). I can find the matches, I cannot... (7 Replies)
I cannot seem to get what should be a simple awk one-liner to work correctly and cannot figure out why. I would like to use patterns from a specific field in one file as regex to search for matching strings in the entire line ($0) of another file.
I would like to output the lines of File2 which... (1 Reply)
Hi,
I need help to match patterns from between two different files and extract region of strings.
inputfile1.fa
>l-WR24-1:1
GCCGGCGTCGCGGTTGCTCGCGCTCTGGGCGCTGGCGGCTGTGGCTCTACCCGGCTCCGG
GGCGGAGGGCGACGGCGGGTGGTGAGCGGCCCGGGAGGGGCCGGGCGGTGGGGTCACGTG... (4 Replies)
Discussion started by: bunny_merah19
4 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)