Bioinformatics

how to make reverse complement of sequence in shell

홍조 2012. 3. 5. 11:23
file content format(tab seperate)
seq_1     atgagagataac
seq_2     tagcgattcaca


output file format(fasta type)
>seq_1
atgagagataac
>seq_1_recom
gttatctctcat

>seq_2
tagcgattcaca
>seq_2_recom
tgtgaatcgcta

$ cat "sequence file" | while read id seq; do echo -e ">$id\n$seq"; recom_seq=$(echo $seq | rev | tr "atgc" "tacg"); recom_id="$id"_revom; echo -e ">$recom_id\n$recom_seq"; done > outout.fasta


ex)
$ awk 'NR<=1300' "sequence file" |grep -v gggg |cut -f2,8 | while read id seq; do echo -e ">$id\n$seq"; recom_seq=$(echo $seq | rev | tr "atgc" "tacg"); recom_id="$id"_revom; echo -e ">$recom_id\n$recom_seq"; done > output.fasta

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