How do I use diamond getseq? #563
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astridfilt
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I found an alternative to getseq, which is seqtk subseq. That gave me what I needed. But I am still curious if I could do it with getseq :) |
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The arguments to |
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Hi :)
I have aligned a bunch of peptides against a diamond database of uniprot sequences using diamond blastp. Now, I want to retrieve the sequences from the diamond database, and I thought I could use diamond getseq for that. But so far, it is not working for me. The commands I have tried are:
diamond getseq --db my_diamond_db.dmnd --seq ["seqID_1" "seqID_2" "seqID_3"]
and
diamond getseq --db my_diamond_db.dmnd --seq "seqID_1" "seqID_2" "seqID_3"
and
diamond getseq --db my_diamond_db.dmnd --seq "seqID_1" "seqID_2" "seqID_3" --out getseq_out
The seqID's are the IDs that are reported as sseqid when I run diamond blastp. The last command did create an output file, but it was empty.
Thank you in advance :)
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