CODEWITHSUNDEEP
sedawk
chas
chas

Reputation: 1645

Edit text file using sed or awk

I have a sample text file as shown below:

>chr1 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>chr10 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>chr11 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>chr12 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>AAEX03020170.1 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATGTGAGAAGATAGCTGAA
>AAEX03022270.1 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATGTGAGAAGATAGCTGAA
>JH373398.1dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATGTGAGAAGATAGCTGAA
>JH373568.1dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATGTGAGAAGATAGCTGAA

The first four starts with chr1, chr10,chr11 and chr12 and the rest starts with a common prefix AAEX and JH.

I would like to delete all the data from lines starting with AAEX and JH i.e. the output should be like:

>chr1 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>chr10 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>chr11 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>chr12 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

The original file has many such lines starting with 'AAEX' and 'JH' and would like to convert as shown above. Any help?

Upvotes: 1

Views: 261

Answers (2)

potong
potong

Reputation: 58478

This might work for you (GNU sed):

sed -r '/^>(AAEX|JH)/{x;/./{x;d};x;s/.*/>chrX/p;h;d};/^>/{x;s/.*//;x}' file

Upvotes: 1

Chris Seymour
Chris Seymour

Reputation: 85865

This should do the trick:

$ awk '/>[AJ]/{if(!f++)print ">chrX";next}NF' file
>chr1 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>chr10 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>chr11 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>chr12 dna:chromosome chromosome:CanFam3.1:1:1:122678785:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>chrX
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATGTGAGAAGATAGCTGAA
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATGTGAGAAGATAGCTGAA
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATGTGAGAAGATAGCTGAA
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATGTGAGAAGATAGCTGAA

Upvotes: 1

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