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Deleting a pattern in UNIX without deleting the entire line


 
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# 1  
Deleting a pattern in UNIX without deleting the entire line

Hi

I have a file:

Code:
r58778.3|SOURCES={KEY=f665931a...,fw,221-705}|ERRORS={16_1:T,30_1:T,56_1:C,57_1:T,59_1:A,101_1:A,115:-,158_1:C,186_1:A,204:-,271_1:T,305:-,350_1:C,368_1:G,442_1:C,472_1:G,477_1:A}|SOURCE_1="Contig_1092402550638"(f665931a359e36cea0976db191ff60ff09cc816e)

I want to retain only r58778.3 and delete the remaining of the entire line so that the new file would be:
Code:
r58778.3

any help, I tried
Code:
sed 's/|SOURCES*//'

but its not the correct command in this case, any advise ?

thanks a lot
Alyaa

Last edited by Scrutinizer; 01-27-2013 at 10:18 AM.. Reason: code tags
# 2  
Please use code tags for code and data samples.

You mean something like this?
Code:
sed '/^r58778\.3|/s/|.*//' file

This User Gave Thanks to elixir_sinari For This Post:
# 3  
Thanks a lot for the prompt reply.

If I try
Code:
sed '/^r*\.*|/s/|.*//' file

, it doesn't work ?? i.e. I want to retain the same patter but for different r* (r58778.3, r56778.1, r21178.2..etc)

thanks again

Last edited by Scrutinizer; 01-27-2013 at 10:18 AM.. Reason: code tags
# 4  
Assuming that I got your requirement right, try:
Code:
sed '/^r[^|][^|]*|/s/|.*//' file

# 5  
Perhaps just:
Code:
cut -d\| -f1

# 6  
thank you very much
# 7  
U have this file:

>VA3401APNWI length=441 xy=0175_0688 region=1 run=R_2011_01_05_12_50_53_
>VA3401B7HKY length=443 xy=0788_1072 region=1 run=R_2011_01_05_12_50_53_


I want to retain only the pattern from ">" till the "space character" before "length". and discard the rest of the line starting "length till the end of the line.

I then want to append a specific string "AT50" to every line in the file.

I tried sed '/^V[^|][^|]*|/s/|.*//' file and sed '/^>[^|][^|]*|/s/|.*//' file but it doesn;t work. Any help please ?

Thank you very much

---------- Post updated at 08:59 AM ---------- Previous update was at 08:57 AM ----------

I want the output to be like that:

>VA3401APNWI tab AT50
>VA3401B7HKY tab AT50
 

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