Sed abandon the X character
I'm looking for a sed command to strip characters from the 11th (and thus keep the first 10) on lines starting with ">". So I want to basically change this file
>LEP004_Iphiclides_podalirius
GCCTCGGCTCACTTGGAAGGTGG
>LEP054_Danaus_plexippus
GGTCGTTGACCTCACTGTTTGCA
Next:
>LEP004_Ip
GCCTCGGCTCACTTGGAAGGTGG
>LEP054_Da
GGTCGTTGACCTCACTGTTTGCA
I tried this command: sed -n '= / {s / ^ (. {10}). * / \ 1 / g; p}' seq.fas> seq_modif.fas, but it just prints the sequence headers (not the sequences DNA)
Thank!
+3
jibbah
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3 answers
You can use this command sed
:
sed '/^>/s/^\(.\{10\}\).*/\1/' file
>LEP004_Ip
GCCTCGGCTCACTTGGAAGGTGG
>LEP054_Da
GGTCGTTGACCTCACTGTTTGCA
+2
anubhava
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This might work for you (GNU sed):
sed '/^>/s/.//11g' file
+2
potong
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Here's the awk
version:
$ awk '/^>/ {$0=substr($0,1,10)} 1' seq.fas
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folkol
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