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grep grab 19 letters from now or a full line

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# 1  
Old 07-31-2012
grep grab 19 letters from now or a full line
Hi,

I have a file like this

Code:
>hg19_chr1_123_456_+
asndbansbdahsjdbfsjhfghjdsghjdghjdjhdghjjdkhfsdkjfhdsjkdkjghkjdhgfjkhjfkf
hasjgdhjsgfhjdsgfdsgfjhdgjhdjhdhjdfhjdfjgfdfbdghjbfjksdhfjsfdghjgdhjgfdjhgd
jhgdfj
>hg19_chr1_123_456_-
akjldshfuiewyruiewehbjhvbdcnmbfhdsjfjdbfhdbhjdbghjfdbghjbdfghjdfbjhbkk
jsdhfjdgjfdgjfdgjkfdhjkfhkjfhjkfjkhkjfskjdfhkjhgjkdgkjfdhgjkfhjkfhgkfhkfkjhgf
dshjghjdg
>hg19_chr2_234_456_+
skjfhdsjkfghdjkghdfjkhgjkfdghjkdfuiertytoierytuireyteiruytueriyteruytierutye
sjhdjashdjahjkdasjkhdajkshdkajshdkashdasruweyriweyrueiwryewrewurewuu
jdhfjkdshf

I want to grep the start of line to be '>' and grab the next 19 letters or the whole line

So, my output will be

Code:
>hg19_chr1_123_456_+
>hg19_chr1_123_456_-
>hg19_chr2_234_456_+

# 2  
Old 07-31-2012
Like this:
Code:
sed -n '/^>/s:\(.\{20\}\).*:\1:p' infile

This User Gave Thanks to elixir_sinari For This Post:
jacobs.smith
# 3  
Old 07-31-2012
Code:
awk '/^>/{print substr($0,1,20)}' input-file

This User Gave Thanks to neutronscott For This Post:
jacobs.smith
# 4  
Old 07-31-2012
@neutron scott. It worked for me. I have more numbers than 3 in the pattern. So, I used 25 instead of 20.

@elixir_sinari - Ur command works too. But, when I increase the 20 to 25, it omits some records. I donno why.

Thanks to both of u.
# 5  
Old 07-31-2012
yah the sed match there says exactly 20, rather than up to 20. I believe that'd need to be \{0,25\}
# 6  
Old 07-31-2012
Quote:
Originally Posted by jacobs.smith
Hi,

I have a file like this

Code:
>hg19_chr1_123_456_+
asndbansbdahsjdbfsjhfghjdsghjdghjdjhdghjjdkhfsdkjfhdsjkdkjghkjdhgfjkhjfkf
hasjgdhjsgfhjdsgfdsgfjhdgjhdjhdhjdfhjdfjgfdfbdghjbfjksdhfjsfdghjgdhjgfdjhgd
jhgdfj
>hg19_chr1_123_456_-
akjldshfuiewyruiewehbjhvbdcnmbfhdsjfjdbfhdbhjdbghjfdbghjbdfghjdfbjhbkk
jsdhfjdgjfdgjfdgjkfdhjkfhkjfhjkfjkhkjfskjdfhkjhgjkdgkjfdhgjkfhjkfhgkfhkfkjhgf
dshjghjdg
>hg19_chr2_234_456_+
skjfhdsjkfghdjkghdfjkhgjkfdghjkdfuiertytoierytuireyteiruytueriyteruytierutye
sjhdjashdjahjkdasjkhdajkshdkajshdkashdasruweyriweyrueiwryewrewurewuu
jdhfjkdshf

I want to grep the start of line to be '>' and grab the next 19 letters or the whole line

So, my output will be

Code:
>hg19_chr1_123_456_+
>hg19_chr1_123_456_-
>hg19_chr2_234_456_+


You said you want the next 19 letters or the whole line.

You have been given two ways to get the '>' and the next 19 letters, but now you seem to want the next 24 characters.

If you want the entirety of lines starting with '>', just use:
Code:
grep '^>' file

otherwise, you need to explain how we are supposed to determine when you want 19 characters, when you want 24 characters, and when you want the whole line.
This User Gave Thanks to Don Cragun For This Post:
jacobs.smith
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