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Add gzipped input support #9

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ninewise opened this issue Oct 31, 2021 · 1 comment
Open

Add gzipped input support #9

ninewise opened this issue Oct 31, 2021 · 1 comment

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@ninewise
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Can you also add a support for gzipped fasta file as input? Should be very easy to implement? Or is is already supported? Think about when we have huge number of genomes downloaded from NCBI, which are all in *.fna.gz format.

(request by @jianshu93 in #5)

@ninewise
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This could be implemented, but I don't see why we would to support it directly. Since FGSrs can take input from standard input, is there a reason not to use zcat? The following command runs FGSrs on a gzipped file:

zcat NC_000913-454.fna.gz | FragGeneScanRs -t 454_10

Of course all other options are supported here as well, just leave out the -s option to read from standard input.

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