pachterlab/ffq

[enhancement] Generate Aspera URL

davetang opened this issue · 1 comments

Hi there,

thank you for the very useful tool. I'd like to suggest a simple feature, which is to generate URLs for downloading with Aspera (supported by the ENA). For example, using --ftp generates the following URLs:

ffq --ftp SRX079566 | grep '"url"'
# snipped
#         "url": "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR292/SRR292241/SRR292241_1.fastq.gz"
#         "url": "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR292/SRR292241/SRR292241_2.fastq.gz"
#         "url": "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR390/SRR390728/SRR390728_1.fastq.gz"
#         "url": "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR390/SRR390728/SRR390728_2.fastq.gz"

Perhaps a new --aspera option that generates the following URLs:

ffq --aspera SRX079566 | grep '"url"'
# snipped
#         "url": "era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR292/SRR292241/SRR292241_1.fastq.gz"
#         "url": "era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR292/SRR292241/SRR292241_2.fastq.gz"
#         "url": "era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR390/SRR390728/SRR390728_1.fastq.gz"
#         "url": "era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR390/SRR390728/SRR390728_2.fastq.gz"

I know I can simply substitute ftp://ftp.sra.ebi.ac.uk/ with era-fasp@fasp.sra.ebi.ac.uk: but I thought it would be nice to add it natively to ffq. It may also inform people of Aspera, which performs much faster downloads.

Cheers,
Dave

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