[SOLVED] Sed is not removing the pattern for a list of headers

Issue

Greeting,

I have following headers in a file with multiple dna sequences

>10 AC_000167.1
>11 AC_000168.1
>12 AC_000169.1
>MT NC_006853.1
>X AC_000187.1
>GPS_000341582.1 NW_003097887.1
>GPS_000341583.1 NW_003097888.1
>GPS_000341584.1 NW_003097889.1
>GPS_000341585.1 NW_003097890.1
>GPS_000341586.1 NW_003097891.1

I am using following sed command to replace everything after the first white space.

sed -i 's/[^(>\d+?MT?X?GPS_\d+\.\d+)]\S..\d+\.\d+//g' newHeader.txt

The output should like this

>10
>11
>12
>MT
>X
>GPS_000341582.1
>GPS_000341583.1
>GPS_000341584.1
>GPS_000341585.1

However the command does not seem to work and does not give any error. How can I fix this?

Solution

With sed:

$ sed -i -E 's/^([^ ]+) .*/\1/' file

The regular expression matches as follows:

Node	Explanation
^	the beginning of the string anchor
(	group and capture to \1:
[^	]+ any character except: space (1 or more times (matching the most amount possible))
)	end of \1
' '	space
.*	any character except \n (0 or more times (matching the most amount possible))

With grep:

grep -oP '^>\S+' file
>10
>11
>12
>MT
>X
>GPS_000341582.1
>GPS_000341583.1
>GPS_000341584.1
>GPS_000341585.1
>GPS_000341586.1

The regular expression matches as follows:

Node	Explanation
^	the beginning of the string anchor
>	>
\S+	non-whitespace (all but \n, \r, \t, \f, and " ") (1 or more times (matching the most amount possible))

If you want to edit in place:

 grep -oP '^>\S+' file | sponge file

Answered By - Gilles Quénot

Answer Checked By - Katrina (WPSolving Volunteer)