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
DIFF(1) 						      General Commands Manual							   DIFF(1)

NAME
diff - differential file comparator SYNOPSIS
diff [ -efbh ] file1 file2 DESCRIPTION
Diff tells what lines must be changed in two files to bring them into agreement. If file1 (file2) is `-', the standard input is used. If file1 (file2) is a directory, then a file in that directory whose file-name is the same as the file-name of file2 (file1) is used. The normal output contains lines of these forms: n1 a n3,n4 n1,n2 d n3 n1,n2 c n3,n4 These lines resemble ed commands to convert file1 into file2. The numbers after the letters pertain to file2. In fact, by exchanging `a' for `d' and reading backward one may ascertain equally how to convert file2 into file1. As in ed, identical pairs where n1 = n2 or n3 = n4 are abbreviated as a single number. Following each of these lines come all the lines that are affected in the first file flagged by `<', then all the lines that are affected in the second file flagged by `>'. The -b option causes trailing blanks (spaces and tabs) to be ignored and other strings of blanks to compare equal. The -e option produces a script of a, c and d commands for the editor ed, which will recreate file2 from file1. The -f option produces a similar script, not useful with ed, in the opposite order. In connection with -e, the following shell program may help maintain multiple versions of a file. Only an ancestral file ($1) and a chain of version-to-version ed scripts ($2,$3,...) made by diff need be on hand. A `latest version' appears on the standard output. (shift; cat $*; echo '1,$p') | ed - $1 Except in rare circumstances, diff finds a smallest sufficient set of file differences. Option -h does a fast, half-hearted job. It works only when changed stretches are short and well separated, but does work on files of unlimited length. Options -e and -f are unavailable with -h. FILES
/tmp/d????? /usr/lib/diffh for -h SEE ALSO
cmp(1), comm(1), ed(1) DIAGNOSTICS
Exit status is 0 for no differences, 1 for some, 2 for trouble. BUGS
Editing scripts produced under the -e or -f option are naive about creating lines consisting of a single `.'. DIFF(1)
All times are GMT -4. The time now is 03:05 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy