How to delete strings in a file?

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06-24-2014

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How to delete strings in a file?

hi, i have a big file like this:

Code:

>s31 length=12 numreads=6 gene=isotig454 status=igo
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk

>c2 length =344 numreads=4 gene=isotig343 status=igoere
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk

>age3 length =32 
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd

.....

for each line with ">", i only want to keep the > and the name, like this:

Code:

>s31 
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk

>c2 
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk

>age3
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd
dfdfdfldfdkdffdlfddflfdjkkkkkkfdgkkgfhghfgkkk
ldfddfdfdfdkkkkkkfdfdkkkksdfdkkkkkkkkkksdfd

.....

how could i obtain this?

the_simpsons

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06-24-2014

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Sure.
Try awk:

Code:

awk 'substr($1,1,1)=="^" 
           {print $1; next}
       {print $0 } '   infile  > tmpfile
# review the tempfile to be sure it is okay.
mv tmpfile infile

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06-24-2014

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Code:

awk '/^>/{NF=1}1' file

OR

Code:

sed 's# .*##' file

Last edited by Yoda; 06-24-2014 at 05:00 PM..

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06-24-2014

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Code:

sed '/^>/s/ .*//' file

Code:

awk '/^>/{$0=$1}1'

Probably this would also work:

Code:

awk '{print $1}' file

Scrutinizer

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06-24-2014

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I have to wonder. If it's a big file, what's the point of using CPU and IO time to remove just a little bit of data?

achenle

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