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ialbert / bio

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invalid command: fasta2vcf #27

Closed gyebra-phs closed 1 year ago

gyebra-phs commented 1 year ago

Hi!

I wanted to use the fasta2vcf option of bio following the instructions in https://www.bioinfo.help/bio-fasta2vcf.html#bio-fasta2vcf

However, I get the following error: invalid command: fasta2vcf.

I'm using version 1.4.0 of bio. Any help would be appreciated!

Thanks

ialbert commented 1 year ago

sorry about that, need to update the docs; the command has been moved to format

bio format --vcf

so the example becomes:

cat aligned.fa | bio format --vcf  > variants.vcf
ialbert commented 1 year ago

the format also a supports a simplified column-based format called --diff that is more amenable to column based operations

gyebra-phs commented 1 year ago

That’s great, thanks for your quick reply! I'll try that.

From: Istvan Albert @.> Sent: Friday, November 11, 2022 4:50:45 PM To: ialbert/bio @.> Cc: Gonzalo Yebra @.>; Author @.> Subject: Re: [ialbert/bio] invalid command: fasta2vcf (Issue #27)

the format also a supports a simplified column-based format called --diff that is more amenable to column based operations

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ialbert commented 1 year ago

The docs have been updated to indicate that the functionality has moved to a different command.