Hello I downloaded more than 10k cds from NCBI and Headers look like this
lcl|DS180867.1_cds_EDM56551.1_2 [protein=hemolysin] [protein_id=EDM56551.1] [location=complement(<1..1012)]
lcl|DS180866.1_cds_EDM56342.1_3 [protein=phosphogluconate dehydratase] [protein_id=EDM56342.1] [location=complement(279..>893)]
lcl|DS180865.1_cds_EDM56120.1_4 [protein=3-hydroxyisobutyrate dehydrogenase] [frame=3] [protein_id=EDM56120.1] [location=complement(162..>559)]
lcl|DS180863.1_cds_EDM56465.1_5 [protein=hemolysin] [protein_id=EDM56465.1] [location=218..>977]
lcl|DS180862.1_cds_EDM56350.1_6 [protein=phosphogluconate dehydratase] [protein_id=EDM56350.1] [location=complement(<1..857)]
i want to extract same all similar sequences (based on the header) into a new fasta file based on protein name (example hemolysin)
please suggest any tool or programme for this
•
written
by
Eva_Maria
1 answer
Hi @akhilvbioinfo, remember SeqKit in your last post?
In which, we sort FASTA sequences by protein names? Here we can also split FASTA records by protein names again.
Same strategy: use flag --id-regexp to specify the protein name as the sequence identifier.
$ seqkit split --by-id --id-regexp "\[protein=(.+?)\]" seqs.fa
[INFO] split by ID. idRegexp: \[protein=(.+?)\]
[INFO] read sequences ...
[INFO] read 5 sequences
[INFO] write 2 sequences to file: seqs.fa.split/seqs.id_hemolysin.fa
[INFO] write 2 sequences to file: seqs.fa.split/seqs.id_phosphogluconate dehydratase.fa
[INFO] write 1 sequences to file: seqs.fa.split/seqs.id_3-hydroxyisobutyrate dehydrogenase.fa
Very simple, right?
See other 18 sub commands provided by SeqKit, you may need it again :)
it's a bug and already fixed since v0.3.8, please download the latest version.
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Have you tried anything?
Yah i tried with AWK but its not working properly
can you post your
awkcode, so that people here can fix the problem in it. I feel that this would be a good idea instead of directly getting a working solution.awk -F "|" '/^>/ {F = $3".fasta"} {print > F}' input.fasta>out.fasta
How do you plan to define similarity based on the header? By the [protein=...] tag?