10 More Discussions You Might Find Interesting
1. UNIX for Beginners Questions & Answers
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
Z represents A, C or G (Except T)
N16 represents any of the four... (3 Replies)
Discussion started by: dineshkumarsrk
2. Shell Programming and Scripting
Here is a file contents :
declare -Ax NEW_FORCE_IGNORE_ARRAY=(="§" ="§" ="§" ="§" ="§" .................. ="§"Here is a pattern
=I want to extract 'NEW_FORCE_IGNORE_ARRAY' which is the whole word before the first occurrence of pattern '='
Is there a better solution than mine :... (3 Replies)
Discussion started by: jcdole
3. Shell Programming and Scripting
I need to extract distinct sequence of letters for example from 136 to 193
Files are quite big, so I would prefer not to use "fold -w1"
Thank you very much
Input file look like this:
1 cttttacctt catgtgtttt tgcagatatt tgttcataat aacatcttct ttttaagtta
61 ttaaaatctt... (4 Replies)
Discussion started by: kamcamonty
4. Shell Programming and Scripting
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
> fefrwefrwef X900
> fefrwefrwef X932
> fefrwefrwef X937... (2 Replies)
Discussion started by: ritakadm
5. Shell Programming and Scripting
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
6. Shell Programming and Scripting
I have hundreds of files to process. In each file
I need to look for a pattern then
extract value(s) from next line and then
search for value(s) selected from point (2) in the same file at a specific position.
HEADER ELECTRON TRANSPORT 18-MAR-98 1A7V
TITLE CYTOCHROME... (7 Replies)
Discussion started by: AshwaniSharma09
7. Shell Programming and Scripting
This is my first post, please be nice. I have tried to google and read different tutorials.
The task at hand is:
Input file input.txt (example)
From this file the task is to grep the -E- and -W- strings that are unique and write a new file... (5 Replies)
Discussion started by: TestTomas
8. Shell Programming and Scripting
I have an one-line file consisting of a sequence of 660 letters. I would like to extract 9-letter blocks iteratively:
first block: ASDFGHJKL
1nd block: SDFGHJKLQ
What I have so far only gives me the first block, can anyone please explain why?
cat... (7 Replies)
Discussion started by: solli
9. Shell Programming and Scripting
I have a pattern like :
Here I need to extract system name and the timestamp and also the numeric number after "-S" i.e 7 here .
I am not very sure of whether I should use sed / awk for this ?:confused:
Priya. (6 Replies)
Discussion started by: priyam
10. Shell Programming and Scripting
I want to be able to extract a sequence of n lines from a file.
ideas, commands and suggestions would be highly appreciated.
Thanks (4 Replies)
Discussion started by: 0ktalmagik