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ncbi / magicblast

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request fo .gz inputs (fastq.gz especially) #23

Closed FTouzain closed 4 years ago

FTouzain commented 4 years ago

Hello, Thank you for the tool. It might be nice to make magicblast accept in input fastq.gz files (both single-end or paired-end) because most of tools accept compressed reads and it avoid to uncompress specifically to this tool. Thank you. Best regards.

boratyng commented 4 years ago

Hi @FTouzain,

Thank you for trying out Magic-BLAST. Magic-BLAST already reads gzipped FASTA and FASTQ files. We need to update documentation to include this fact. Please, try this for example

magicblast -query reads.fastq.gz -infmt fastq -db genome

No need for additional parameters. Magic-BLAST recognizes compressed files by the .gz extension, so the compressed file names must end with .gz and it works only for gzip compression. Please, let me know if it does not work for you.

Thanks, Greg

FTouzain commented 4 years ago

Many thanks, I will try. Best regards Fabrice