saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO
https://saketkc.github.io/pysradb
BSD 3-Clause "New" or "Revised" License
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[BUG] ENA url missing #163

Closed Maarten-vd-Sande closed 2 years ago

Maarten-vd-Sande commented 2 years ago

Describe the bug

I feel like I never get ena fastq urls anymore? DRR138997 should be downloadable from ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR138/DRR138997/DRR138997_1.fastq.gz, but pysradb doesn't find it

import pysradb
web = pysradb.SRAweb()
web.sra_metadata(["DRR138997"], detailed=True)
  run_accession study_accession                                        study_title experiment_accession  ... ena_fastq_http_2 ena_fastq_ftp ena_fastq_ftp_1 ena_fastq_ftp_2
0     DRR138976       DRP004498  Accessible chromatin landscapes of vertebrate ...            DRX131714  ...             <NA>          <NA>            <NA>            <NA>
1     DRR138997       DRP004498  Accessible chromatin landscapes of vertebrate ...            DRX131714  ...             <NA>          <NA>            <NA>            <NA>
saketkc commented 2 years ago

Thanks - this was due to an upstream change in the ENA search url. 1.4.2 should fix it.

Maarten-vd-Sande commented 2 years ago

Awesome, thanks!