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[Feature request] Support for stdin #35
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Hi @jolespin, I'm always a bit reluctant to add more features to the CLI as the primary goal of Pyrodigal is to be used as a library when possible, and because I don't want to mimic the Prodigal CLI 100% (like the broken GenBank output for instance). However, I had a look at your code architecture, and while I believe it would be best not to invoke Pyrodigal as a subprocess, I understand why it's organized like that. I'd accept a PR if you want to try, otherwise I'll have a look but can't promise when. |
Can you point me in the direction of the executable I should edit? I thought it was the _cli.py but noticed there are some arguments that are not usable in the cli such as the number of threads. |
No, you're right, it's indeed the |
Have you got any other requests about stdin support? |
Not really, just make the |
I'm trying to replace
prodigal
withpyrodigal
in my VEBA binning-prokaryotic.py module. I use stdin because I do some filtering on contig lengths w/seqkit
before I do gene calls and don't want to rewrite the contigs b/c that's a lot of space.Can you add support for reading fasta input as
stdin
?Preferably it no input is provided then assume it's
stdin
which is the current functionality ofprodigal
.Also, I just noticed there's not support for
stdout
. Can you add this functionality as well? This is the default functionality ofprodigal
and it's quite useful. I use it to pipe directly into this script: https://github.com/jolespin/veba/blob/devel/src/scripts/append_geneid_to_prodigal_gff.py which adds the gene id.The text was updated successfully, but these errors were encountered: