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Extract sequence from fasta file

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# 1  
Old 10-15-2013
Extract sequence from fasta file
Hi,

I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .

Code:
input 

> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937
AGAGGGAATTGG
AGGAGACTTTAG
GGTTCTCTTC

So if my input parameter is X937 I get an output of
Code:
> fefrwefrwef X937
AGAGGGAATTGG
AGGAGACTTTAG
GGTTCTCTTC

If my input parameter is X932 I should get

Code:
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC

If input is X9, I should get the entire file.
# 2  
Old 10-15-2013
Using awk :

Code:
awk -v F="X9" '$1 ~ F {printf "%s", RS $0} ' RS='> ' FS="\n" infile

# 3  
Old 10-15-2013
Very simple one:
Code:
awk '/X937/' RS='> ' input

...using variable:
Code:
awk -v P="$s" '$0~P' RS='> ' input

... adding leading RS:
Code:
awk -v P="$s" '!c++{printf RS}$0~P' RS='> ' input

Code:
$ s=X937
$ awk -v P="$s" '$0~P' RS='> ' input
fefrwefrwef X937
AGAGGGAATTGG
AGGAGACTTTAG
GGTTCTCTTC

Last edited by ctsgnb; 10-15-2013 at 08:00 PM..
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