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
BP_DBSPLIT(1p)						User Contributed Perl Documentation					    BP_DBSPLIT(1p)

NAME
dbsplit - script to split an input set of database(s) into smaller pieces SYNOPSIS
dbsplit.PLS --size 50 [-i inputfile] [-if inputformat] [-of outputformat] [--prefix outputprefix] [ < file1 file 2 OR file1 file2] DESCRIPTION
This script will take as input a list of filenames or a single file or from STDIN a sequence database and split the database into separate files of X numbers of sequences. You specify X with the "--size/-s" parameter. The input and output sequence format is any that is supported by bioperl (fasta,embl,genbank,gcg, swissprot, etc). You can specify the input data either as a single file with -i filename, or as a single file as an argument like % dbsplit file1 file2 or as a list of sequence data with % cat file1 file2 file3 | dbsplit You'll want to use the "--prefix" to specify what the output prefix will be. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR
Jason Stajich, jason-at-bioperl-dot-org perl v5.14.2 2012-03-02 BP_DBSPLIT(1p)
All times are GMT -4. The time now is 08:25 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy