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extract lines from data

 
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# 1  
Old 04-05-2010
extract lines from data
I have a file that looks like this:

Code:
 >cel-miR-35 MIMAT6 C eles le
UCACCGGGUGGAAACUAGCAGU
>hsa-let-7a MI062 H sa
UGAGGUAGUAGGUUGUAUAGUU
>cel-miR-36 M007 Ca ele 
UCACCGGGUGAAAAUUCGCAUG
>hsa-let-7b MI63 Hmo sns le
UGAGGUAGUAGGUUGUGUGGUU

I would like to extract all the lines that start with '>hsa' and the next line so the output should look like this:

Code:
 >hsa-let-7a MI062 H sa
UGAGGUAGUAGGUUGUAUAGUU
>hsa-let-7b MI63 Hmo sns le
UGAGGUAGUAGGUUGUGUGGUU

# 2  
Old 04-06-2010
Code:
grep '^>hsa' file

# 3  
Old 04-06-2010
Quote:
Originally Posted by anbu23
Code:
grep '^>hsa' file

i need the next line also.
# 4  
Old 04-06-2010
Code:
 grep -A1 hsa sample

# 5  
Old 04-06-2010
Or if your grep doesn't support -A option...

Code:
awk '/^>hsa/{print;getline;print}' infile

# 6  
Old 04-06-2010
Code:
sed -n '/^>hsa/{N;p;}' file

# 7  
Old 04-06-2010
Quote:
Originally Posted by phoenix_nebula
Code:
 grep -A1 hsa sample

Thank you, it does what I want.
I have a follow up question: how do I combine the -A option with the -v option to get all the line except the one statrting with '>hsa' and the next line?

infile
Code:
>cel-miR-35 MIMAT6 C eles le
UCACCGGGUGGAAACUAGCAGU
>hsa-let-7a MI062 H sa
UGAGGUAGUAGGUUGUAUAGUU
>cel-miR-36 M007 Ca ele 
UCACCGGGUGAAAAUUCGCAUG
>hsa-let-7b MI63 Hmo sns le
UGAGGUAGUAGGUUGUGUGGUU

outfile should look like this:
Code:
 >cel-miR-35 MIMAT6 C eles le
UCACCGGGUGGAAACUAGCAGU
>cel-miR-36 M007 Ca ele 
UCACCGGGUGAAAAUUCGCAUG

I tried:
Code:
grep -A1 -v hsa infile

the outfile was the same as the infile.

---------- Post updated at 09:55 AM ---------- Previous update was at 09:48 AM ----------
Quote:
Originally Posted by malcomex999
Or if your grep doesn't support -A option...

Code:
awk '/^>hsa/{print;getline;print}' infile

I also tried to print only lines which do NOT match '>hsa' with
Code:
awk '!/^>hsa/{print;getline;print}' infile

I got
Code:
>cel-miR-35 MIMAT6 C eles le
UCACCGGGUGGAAACUAGCAGU
UGAGGUAGUAGGUUGUAUAGUU
>cel-miR-36 M007 Ca ele 
UCACCGGGUGAAAAUUCGCAUG
>hsa-let-7b MI63 Hmo sns le
UGAGGUAGUAGGUUGUGUGGUU
UGAGGUAGUAGGUUGUGUGGUU

I should get
Code:
>cel-miR-35 MIMAT6 C eles le
UCACCGGGUGGAAACUAGCAGU
>cel-miR-36 M007 Ca ele 
UCACCGGGUGAAAAUUCGCAUG

 
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