Identify the overlapping and non overlapping regions
I have 2 input files file1 and file2 each containing 5 columns. The first column contains the chromosomes (range from 1-19,X of which only chr1 and chr2 were shown in example).
what i want to do is
condition1 if chr pos1 and pos2 in both files overlap
then i want to compare the pos3 and pos4. if they (pos3 and pos4) overlap i want to output them to output_1file
and
if they (pos3 and pos4) wont overlap then output to output_2 file.
so if we compare file 1 with file2
my definition of overlap
The positions need not be exactly same. They should contain common region atleast by 1bp(base pair).
Hi,
I am a newbie in unix programming so maybe this is a simple question.
I would like to know how can I make a script that outputs only the values that are not between any given start and end positions
Example
file1:
2 30
40 80
82 100
file2:
ID1 1
ID2 35
ID3 80
ID4 81
ID6 160... (1 Reply)
Hi,
I want to match and print columns that match.
So my file looks like this:
h1 20 30 h1 25 27
h2 50 70 h2 90 95
h2 60 80 h2 70 75
h3 130 150 h3 177 190
h4 140 190 h4 300 305
So there are 6 columns. Column 1 and 4 are names. I am able to get the... (2 Replies)
Hi Everyone!
I was wondering if there's an easy way to have terminals (gnome-terminal for instance) be open in such a way that they're not overlapping each other?
I suppose I could play around with the --geometry option but that would imply me checking whether a terminal is already at a given... (3 Replies)
I am making a game, but I can't figure out how to put one image over the other. The background of the front image, covers up the picturebox under it.
For example, I have two fish images, but when one is in front of the other, its background covers up the other fish.
I attached a picture as an... (1 Reply)
hey guys,
i'm having trouble with a real time multi threaded program that uses lots of shared memory on solaris 8. it sometime crashes out of the blue, a randomness that suggests some sort of memory leak or shared memory overlap.
any tips? freeware or otherwise useful software?
any way i can... (2 Replies)
Greetings folks,
I have a rather lengthy list of banned IP ranges in iptables. Initially it was constructed as a rather ad-hoc affair, then later I discovered a site which had IP Block By Country lists, and imported several into iptables.
If possible, I'd like to be able to verify if the list... (0 Replies)
Dear Gurus,
I have 57 tab-delimited different text files, each one containing entries in 3 columns. The first column in each file contains names of objects. Some names are present in more than one file. I would like to find those names and store them in a separate text file, preferably with a... (6 Replies)
I have 2 files; file 1 having smaller positions that overlap with the positions with positions in file2.
file1
aaa 20 22 apple
aaa 18 25 banana
aaa 12 30 grapes
aaa 22 25 melon
file2
aaa 18 26 cdded
aaa 10 35 abcde
I want to get something like this
output
aaa 18 26 cdded banana... (4 Replies)
Discussion started by: anurupa777
4 Replies
LEARN ABOUT OPENSOLARIS
comm
comm(1) User Commands comm(1)NAME
comm - select or reject lines common to two files
SYNOPSIS
comm [-123] file1 file2
DESCRIPTION
The comm utility reads file1 and file2, which must be ordered in the current collating sequence, and produces three text columns as output:
lines only in file1; lines only in file2; and lines in both files.
If the input files were ordered according to the collating sequence of the current locale, the lines written will be in the collating
sequence of the original lines. If not, the results are unspecified.
OPTIONS
The following options are supported:
-1 Suppresses the output column of lines unique to file1.
-2 Suppresses the output column of lines unique to file2.
-3 Suppresses the output column of lines duplicated in file1 and file2.
OPERANDS
The following operands are supported:
file1 A path name of the first file to be compared. If file1 is -, the standard input is used.
file2 A path name of the second file to be compared. If file2 is -, the standard input is used.
USAGE
See largefile(5) for the description of the behavior of comm when encountering files greater than or equal to 2 Gbyte ( 2^31 bytes).
EXAMPLES
Example 1 Printing a list of utilities specified by files
If file1, file2, and file3 each contain a sorted list of utilities, the command
example% comm -23 file1 file2 | comm -23 - file3
prints a list of utilities in file1 not specified by either of the other files. The entry:
example% comm -12 file1 file2 | comm -12 - file3
prints a list of utilities specified by all three files. And the entry:
example% comm -12 file2 file3 | comm -23 -file1
prints a list of utilities specified by both file2 and file3, but not specified in file1.
ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of comm: LANG, LC_ALL, LC_COLLATE,
LC_CTYPE, LC_MESSAGES, and NLSPATH.
EXIT STATUS
The following exit values are returned:
0 All input files were successfully output as specified.
>0 An error occurred.
ATTRIBUTES
See attributes(5) for descriptions of the following attributes:
+-----------------------------+-----------------------------+
| ATTRIBUTE TYPE | ATTRIBUTE VALUE |
+-----------------------------+-----------------------------+
|Availability |SUNWesu |
+-----------------------------+-----------------------------+
|CSI |enabled |
+-----------------------------+-----------------------------+
|Interface Stability |Standard |
+-----------------------------+-----------------------------+
SEE ALSO cmp(1), diff(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5)SunOS 5.11 3 Mar 2004 comm(1)