I have a csv file from which I extract data relevant to me. These are reference numbers on the one hand and genetic information in the form of the letters G, A, T and C on the other.
1,S188823,188823,,,,ACTCTCGA,,CTGTACCA,ID23, 1,S189843,189843,,,,ACCCTGGA,,CTTGTACA,ID23, ...
The information relevant to me is
From each line. Duplicates must be removed in the process. Also the first two lines have to be truncated.
This is what I currently do:
cat File.csv | cut -d "," -f 3,9,7 | uniq | sed -e '1d' -e '2d'
The result looks like this:
188823,ACTCTCGA,CTGTACCA 189843,ACCCTGGA,CTTGTACA ...
But now two things have to be done, which I fail at. Field 3 and field 2 have to be swapped
188823,CTGTACCA,ACTCTCGA 189843,CTTGTACA,ACCCTGGA ...
and now from field2 the bases have to be "reverse complemented" This means that each A becomes a T, each C becomes a G, each G becomes a C and each T becomes an A and the sequence order is reversed. So,
The final result must then look like this:
I hope it is understandable and you can help me. Some help about reverse complement building can be found here: revcomp builder online