Login or Register to Ask a Question and Join Our Community


UNIX for Dummies Questions & Answers

SED and wildcards

 
Thread Tools Search this Thread
Top Forums UNIX for Dummies Questions & Answers SED and wildcards
# 1  
Old 09-10-2010
SED and wildcards
I am using this code to locate and modify one particular ID in a file containing thousands of entries
Code:
sed 's/^>OldID/>NewID/g' Infile > Outfile

How can I modify the code so I can rename all old IDs to a new unique ID?
I tried this
Code:
sed 's/^>*/>NewID/g' Infile > Outfile

but it did not work.
Thanks in advance
# 2  
Old 09-10-2010
Can you post sample OldIDs?
# 3  
Old 09-10-2010
There you go
Quote:
>C0/C0_s15_C05_0_485
ATTAGATACCCGGGTAGTCCACGCCCTAAACGATGTCAACTGGTTGTTGGGTCTTCACTGACTCAGTAACGAAGCTAACG
CGTGAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAT
GATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCCACCTTTGACATGTACGGAATTTGCCAGAGATGGCTTAGTGC
TCGAAAGAGAACCGTAACACAGGTGCTGCATGG
>C0/C0_s15_C05_73_86
ATTAGATACCCCGGTAGTCCACGCCCTAAACGATGTCAACTGGTTGTTGGGTCTTCACTGACTCAGTAACGAAGCTAACG
CGTGAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAT
GATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCCACCTTTGACATGTACGGAATTTGCCAGAGATGGCTTAGTGC
TCGAAAGAGAACCGTAACACAGGTGCTGCATGG
>C0/C0_s15_C05_170_500
ATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTGGTTGTTGGGTCTTCACTGACTCAGTAACGAAGCTAACG
CGTGAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAT
GATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCCACCTTTGACATGTACGGAATTTGCCAGAGATGGCTTAGTGC
TCGAAAGAGAACCGTAACACAGGTGCTGCATGG
>C0/C0_s15_C05_239_262
ATTAGATACCCGGGTAGTCCACGCCCTAAACGATGTCAACTGGTTGTTGGGTCTTCACTGACTCAGTAACGAAGCTAACG
CGTGAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAT
GATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCCACCTTTGACATGTACGGAAGTTACCAGAGATGGTTTCGTGC
TCGAAAGAGAACCGTAACACAGGTGCTGCATGGCTGTCGTC
>C0/C0_s15_C05_308_278
ATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTGGTTGTTGGGTCTTCACTGACTCAGTAACGAAGCTAACG
CGTGAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAT
GATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCCACCTTTGACATGTACGGAAGTTACCAGAGATGGTTTCGTGC
TCGAAAGAGAACCGTAACACAGGTGCTGCATGGCTGTCG
>C0/C0_s15_C05_412_130
ATTAGATACCCCGGTAGTCCACGCCCTAAACGACGTCAACTGGTTGTTGGGTCTTAACTGACTCAGTAACGAAGCTAACG
CGTGAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAT
GATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCCACCTTTGACATGTACGGAAGGATCCAGAGATGGATTTGTGC
TCGAAAGAGAACCGTAACACAGGTGCTGCATGGCTGTCGTC
>C0/C0_s15_C05_443_221
ATTAGATACCCTGGTAGTCCACGCCCTAAACGACGTCAACTGGTTGTTGGGTCTTAACTGACTCAGTAACGAAGCTAACG
CGTGAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAT
GATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCCACCTTTGACATGTACGGAAGGATCCAGAGATGGATTTGTGC
TCGAAAGAGAACCGTAACACAGGTGCTGCATGGCTGTCG
# 4  
Old 09-10-2010
Code:
sed 's/^>.*/>NewID/g' Infile > Outfile

This User Gave Thanks to bartus11 For This Post:
Xterra
# 5  
Old 09-10-2010
bartus
Thank you very much! It works like a charm.
One pretty quick question, how can I modify the code if I would like to replace the new IDs with consecutive numbers let say 1,2,3,4, etc or NewID1, NewID2, NedID3, etc..
Thanks once again!
# 6  
Old 09-10-2010
For this I'd use AWK :P
Code:
awk '/>/{i++;sub(".*","NewID"i)}1' Infile > Outfile

This User Gave Thanks to bartus11 For This Post:
Xterra
# 7  
Old 09-10-2010
Great! Thanks!
Code:
awk '/>/{i++;sub(".*",">NewID"i)}1' Infile > Outfile

 
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Using Wildcards in scp

to scp using windcards you use the following : scp 'hostname:/home/username/diff_201110*' . Enjoy ! (0 Replies)
Discussion started by: phpsnook
0 Replies

2. UNIX for Advanced & Expert Users

Wildcards

These 2 websites do a GREAT job of explaining different types of wildcards. I learned about the categories of characters which I never knew about at all. GNU/Linux Command-Line Tools Guide - Wildcards GREP (1 Reply)
Discussion started by: cokedude
1 Replies

3. UNIX for Dummies Questions & Answers

wildcards in path

Is there some rule about using wildcards in path? Say I want to create a file, but one of the directories in the path is called 1433d.default and on different machines it will be called <some other string>.default touch ~/Library/Application/*.default/myfile In theory I thought that... (5 Replies)
Discussion started by: glev2005
5 Replies

4. Shell Programming and Scripting

SED with Wildcards and Special Characters

Hi All, Need you guys' help to achieve the following: I have some strings and i wish to threw off the end part that's in the file path. From: /directoryname1/subdirectoryname1/abc.txt /directoryname2/subdirectoryname2/defggf.txt To: /directoryname1/subdirectoryname1/... (7 Replies)
Discussion started by: Radeon
7 Replies

5. Shell Programming and Scripting

Use wildcards in a script

Hello I have this script: #!/bin/ksh INPUTFILE=$1 TEMPFILE=$INPUTFILE.$$ OUTPUTFILE=$INPUTFILE.new # nr of arguments has to be 1 if then echo "\nUsage: $0 inputfile\n" return 1 fi # inputfile must exist and be readable if then (13 Replies)
Discussion started by: emferrari
13 Replies

6. UNIX for Dummies Questions & Answers

wildcards NOT

Hi All Please excuse another straightforward question. When creating a tar archive from a directory I am attempting to use wildcards to eliminate certain filetypes (otherwise the archive gets too large). So I am looking for something along these lines. tar -cf archive.tar * <minus all *.rst... (5 Replies)
Discussion started by: C3000
5 Replies

7. Shell Programming and Scripting

Wildcards in SED

Hi Folks Quick one I can't seem to figure out sed wildcards.. I need to replace a string such as "From here.....to here". I would think the command would look like: sed 's/From here*to here/new text/g' or sed 's/From here\*to here/new text/g' But it's not working for me. Thanks in... (5 Replies)
Discussion started by: HealthyGuy
5 Replies

8. UNIX for Dummies Questions & Answers

ls with wildcards

ok, I'm trying to write a script file that lists files with specific elements in the name into a txt file, it looks like this ls s*.dat > file_names.txt can't figure out whats wrong with that line, any ideas? thanks in advance (10 Replies)
Discussion started by: benu302000
10 Replies

9. UNIX for Dummies Questions & Answers

wildcards

when writing a shell script (bourne) and using a unix command like 'ls' is there anything special you need to do to use a wildcard (like *)? (3 Replies)
Discussion started by: benu302000
3 Replies

10. UNIX for Dummies Questions & Answers

Wildcards in VI

I'm trying to delete lines from a large text file using VI. Every line that I am wanting to delete start with 'S' - all others do not. (A list of users) I've tried using * but doesn't seem to like it...any ideas... Doesn't have to be VI - but I'm better with VI than sed/awk. (8 Replies)
Discussion started by: peter.herlihy
8 Replies
Login or Register to Ask a Question