Sponsored Content
Full Discussion: Sequence extraction
Top Forums Shell Programming and Scripting Sequence extraction Post 302951322 by harpreetmanku04 on Wednesday 5th of August 2015 06:21:37 AM
Old 08-05-2015
may be that entries would be at the bottom of the file actually sir, i just copied and posted very few entries from file1 and file2 may be matched would be skipped. i cant paste my whole data file here i have 4565005 sequence entries in my data.

and about negative value, please provide me the script for like 300 250 = 50
no problem if there is 250-300 =-50 i will correct it and will then apply script.
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Help with tar extraction!

I have this tar file which has files of (.ksh, .ini &.sql) and their hard and soft links. Later when the original files and their directories are deleted (or rather lost as in a system crash), I have this tar file as the only source to restore all of them. In such a case when I do, tar... (4 Replies)
Discussion started by: manthasirisha
4 Replies

2. Shell Programming and Scripting

AWK extraction

Hi all, I have a data file from which i would like to extract only certain fields, which are not adjacent to each other. Following is the format of data file (data.txt) that i have, which has about 6 fields delimited by "|" HARRIS|23|IT|PROGRAMMER|CHICAGO|EMP JOHN|35|IT|JAVA|NY|CON... (2 Replies)
Discussion started by: harris2107
2 Replies

3. Shell Programming and Scripting

extraction of last but one char

I need to extract the character before the last "|" in the following lines, which are 'N' and 'U'. The last "|" shouldn't be extracted. Also the no.s of "|" may vary in a line, but I need only the character before the last one. ... (5 Replies)
Discussion started by: hidnana
5 Replies

4. Shell Programming and Scripting

Regex extraction

Hello, I need your help to extract text from following: ./sherg_fyd_rur:blkabl="R23.21_BL2008_0122_1" ./serge_a75:rlwual="/main/r23.21=26-Mar-2008.05:00:20UTC@R11.31_BL2008_0325" ./serge_a75:blkabl="R23.21_BL2008_0325" ./sherg_proto_npiv:bkguals="R23.21_BL2008_0302 I80_11.31_LR" I... (11 Replies)
Discussion started by: abdurrouf
11 Replies

5. Programming

extraction from a path

Hi, Can you help me on this two problems? how can i get : from input: /ect/exp/hom/bin ==> output: exp and from input: aex1234 =====>output: ex thanks, (1 Reply)
Discussion started by: yeclota
1 Replies

6. Shell Programming and Scripting

extraction

I have following input @xxxxxx@ I want to extract what's between @....@ that is : xxxx using SED command (6 Replies)
Discussion started by: xerox
6 Replies

7. UNIX for Dummies Questions & Answers

fast sequence extraction

Hi everyone, I have a large text file containing DNA sequences in fasta format as follows: >someseq GAACTTGAGATCCGGGGAGCAGTGGATCTC CACCAGCGGCCAGAACTGGTGCACCTCCAG GCCAGCCTCGTCCTGCGTGTC >another seq GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT GACATTTTCATTACTACCATTTTGGAGTACA >seq3450... (4 Replies)
Discussion started by: Fahmida
4 Replies

8. Shell Programming and Scripting

find common entries and match the number with long sequence and cut that sequence in output

Hi all, I have a file like this ID 3BP5L_HUMAN Reviewed; 393 AA. AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3; DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot. DT 05-JUL-2004, sequence version 1. DT 05-SEP-2012, entry version 71. FT COILED 59 140 ... (1 Reply)
Discussion started by: manigrover
1 Replies

9. Shell Programming and Scripting

String Extraction

I am trying to extract a time from the below string in perl but not able to get the time properly I just want to extract the time from the above line I am using the below syntax x=~ /(.*) (\d+)\:(\d+)\:(\d+),(.*)\.com/ $time = $2 . ':' . $3 . ':' . $4; print $time Can... (1 Reply)
Discussion started by: karan8810
1 Replies

10. Shell Programming and Scripting

Extraction of upstream and downstream regions from long sequence file

Hello, here I am posting my query again with modified data input files. see my query is : i have two input files file1 and file2. file1 is smalldata.fasta >gi|546671471|gb|AWWX01449637.1| Bubalus bubalis breed Mediterranean WGS:AWWX01:contig449636, whole genome shotgun sequence... (20 Replies)
Discussion started by: harpreetmanku04
20 Replies
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)
All times are GMT -4. The time now is 06:02 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy