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Need help with searching and copying in a text file

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# 1  
Old 04-26-2011
Need help with searching and copying in a text file
Hi,

I need help searching through a large text file. I need to find a certain string within the text, and copy each line until another string appears.


The file looks like this:
Code:
>scf15164843
ATTAAAGGNNNGGAATTTCCCCAA
ATTACCGGCTTTAAANNNTTACCC
>scf15154847
CCGGGNNNTTTAAACCCGNGNGCC
ATTANCGCGCGCATTAAATTTAAA
CTGTGTGAAAATCCGATAAGAGAG
GTGTGTGTGTTTGGTTTTTAAAAAA
>scf15164847
TTAGGTTGGAAAAAGGGTTTTAAG
GAAGGTTTTGGAAAAGTTAACCNN

And I need the output to be in another file as:
Code:
>scf15154847
CCGGGNNNTTTAAACCCGNGNGCC
ATTANCGCGCGCATTAAATTTAAA
CTGTGTGAAAATCCGATAAGAGAG
GTGTGTGTGTTTGGTTTTTAAAAAA

The part I need will always be between >scf######### and a > from another sequence.

Thanks in advance!
# 2  
Old 04-26-2011
Code:
nawk -v str='>scf15154847' '$0 ~ str {f=1;print;next} f &&!/^>/{print;next}f{f=0}' myFile

Last edited by vgersh99; 04-26-2011 at 06:50 PM..
This User Gave Thanks to vgersh99 For This Post:
repiv
# 3  
Old 04-26-2011
This will save the sections in separate files named out.<numberAfterscf>:
Code:
awk '$0{print ">scf"suff"\n" $0 > "out."suff}
       {suff=RT; sub(/>scf/,"",suff); sub(/\n/,"",suff)}
    ' RS='>scf[0-9]*\n*' ORS="" myFile

Last edited by mirni; 04-26-2011 at 09:48 PM..
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