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Shell Programming and Scripting

modifying a row

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# 1  
Old 06-08-2010
modifying a row
I want to modify a file by deleting certain characters. The file looks like this:

Code:
>ctg86 org=S_bayanus] moltype=genomictg] ctgontig=ctg86]
RRRRRRRRRRRRRRRRRRRRRRRRRRRRTTTTTTTTTTTTTTTTTTTTTTTYYYYYYYYYYYYYYYYYYYYFFFFFFFFFFFGGGGGGGGGHHHHH
>ctg86 org=S_bayanus] moltype=genomictg] ctgontig=ctg86]
HHIIIIIIIIIMMMMMMMMMMMRRRRRRRRRRRRTTTTTTTTTTTTTTTTTTTTTTTT

I want to modify the lines with the > so the output looks like this

Code:
>ctg86
RRRRRRRRRRRRRRRRRRRRRRRRRRRRTTTTTTTTTTTTTTTTTTTTTTTYYYYYYYYYYYYYYYYYYYYFFFFFFFFFFFGGGGGGGGGHHHHH
>ctg86
HHIIIIIIIIIMMMMMMMMMMMRRRRRRRRRRRRTTTTTTTTTTTTTTTTTTTTTTTT

thanks
Phil
# 2  
Old 06-08-2010
Code:
awk ' { if ( $0~/>/  ) { print $1 } else {print } }' inputfile

# 3  
Old 06-08-2010
Quote:
Originally Posted by phil_heath
I want to modify a file by deleting certain characters. The file looks like this:

Code:
>ctg86 org=S_bayanus] moltype=genomictg] ctgontig=ctg86]
RRRRRRRRRRRRRRRRRRRRRRRRRRRRTTTTTTTTTTTTTTTTTTTTTTTYYYYYYYYYYYYYYYYYYYYFFFFFFFFFFFGGGGGGGGGHHHHH
>ctg86 org=S_bayanus] moltype=genomictg] ctgontig=ctg86]
HHIIIIIIIIIMMMMMMMMMMMRRRRRRRRRRRRTTTTTTTTTTTTTTTTTTTTTTTT

I want to modify the lines with the > so the output looks like this

Code:
>ctg86
RRRRRRRRRRRRRRRRRRRRRRRRRRRRTTTTTTTTTTTTTTTTTTTTTTTYYYYYYYYYYYYYYYYYYYYFFFFFFFFFFFGGGGGGGGGHHHHH
>ctg86
HHIIIIIIIIIMMMMMMMMMMMRRRRRRRRRRRRTTTTTTTTTTTTTTTTTTTTTTTT

thanks
Phil
Assuming that each line that you want to modify starts with the same string of ">ctg86" you can do something like this:

Code:
sed -e 's/\(>ctg86\).*/\1/' file

# 4  
Old 06-08-2010
Code:
awk '{print ($0~/>/)?$1:$0}' urfile

or
Code:
awk '/>/ {$0=$1}1' urfile

# 5  
Old 06-08-2010
Quote:
Originally Posted by malcolmpdx
Assuming that each line that you want to modify starts with the same string of ">ctg86" you can do something like this:

Code:
sed -e 's/\(>ctg86\).*/\1/' file

Actually, to be precise, you'd probably want to anchor that string at the beginning of a line:

Code:
sed -e 's/^\(>ctg86\).*/\1/' file

just to handle a situation where the same string occurred later in a line.
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