combine subsets for human subcatalog

[Ulrike Löber]

Dear Luis,

for a new project, we would like to run different human body sites to the same gmgc subset containing all human body sites included in gmgc. Is it possible to pipe the subsets or construct a "all human" subcatalog?

Yours sincerely,

Ulrike

[Luis Pedro Coelho]

This is the sort of thing that would still be a bit of a hassle a few years ago, but quite trivial nowadays. Yes, you can just concatenate all the sequences together and making sure you are not repeating them, something like

seen = set()

output = open('human-combined.fna', 'wt')

for fna in glob('*human*.fna.gz'):

    for h,seq in fasta_iter(fna):

        if h in seen: continue

        seen.add(h)

        out.write(f">{h}\n{seq}\n")

HTH, Luis

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Luis Pedro Coelho | Queensland University of Technology | https://luispedro.org

https://orcid.org/0000-0002-9280-7885