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A long short but is there a way to copy the end of select lines and append the text to that line. What I want to achieve is this.
what I have
>13_gnd
atcg
>14_galF
atgc
what I want
>13_gnd_gnd
atcg
>14_galF_galF
atgc
So all lines starting with >copy the last word and append to the end of the line. Thanks.
$ sed 's/_[^_]*$/&&/' file
>13_gnd_gnd
atcg
>14_galF_galF
atgc
The sed substitution will match the last underscore on each line and whatever is after it, to the end of the line. This is what the pattern _[^_]*$ does ("match an underscore possibly followed by other non-underscore characters, and the end of line"). It will replace this (including the underscore) with whatever was matched, twice (this is what && does in the replacement bit).
Since this appears to be a file in Fasta format, and since genomic sequences can't contain underscores, no special test is needed for > at the beginning of the line.
>" and we don't don't whether the undercore can appear in other lines, too, the safe solution would be sed '/^>/s/_[^_]*$/&&/' file. However, I like the && replacement. (-:
Jun 22, 2017 at 12:52
>) can't contain underscores.
Short awk solution:
awk -F'_' '$0~/^>/{ $0=$0 FS $NF }1' file
The output:
>13_gnd_gnd
atcg
>14_galF_galF
atgc
Details:
-F'_' - field separator
$0~/^>/ - performs an action if the line starts with >
$0=$0 FS $NF - appends the last field value to the end
