Download links not active

[bschilder]

Hi,

Thanks for the resource!

I'm went to go use the API but noticed the download links don't seem to actually be active.

https://www.personalgenomes.org.uk/api/#/

def get_api_data(endpoint, url="https://www.personalgenomes.org.uk/api/v1.3/"):
    response = requests.get(url + endpoint)
    return response.json()
urls = get_api_data("all_download_url")
urls

[{'hex_id': 'uk33D02F',
  'data': [{'type': 'WGS Fastq (_1)',
    'download_url': 'ftp.sra.ebi.ac.uk/vol1/fastq/ERR172/008/ERR1726428/ERR1726428_1.fastq.gz'},
   {'type': 'WGS Fastq (_2)',
    'download_url': 'ftp.sra.ebi.ac.uk/vol1/fastq/ERR172/008/ERR1726428/ERR1726428_2.fastq.gz'},
   {'type': 'WGS Bam',
    'download_url': 'ftp.sra.ebi.ac.uk/vol1/run/ERR172/ERR1726428/FR07961005.bam'},
   {'type': 'VCF MD5',
    'download_url': 'ftp.sra.ebi.ac.uk/vol1/ERZ389/ERZ389534/ERZ389534.md5'},
   {'type': 'VCF Tabix Index',
    'download_url': 'ftp.sra.ebi.ac.uk/vol1/ERZ389/ERZ389534/FR07961005.pass.recode.vcf.gz.tbi'},
   {'type': 'VCF',
    'download_url': 'ftp.sra.ebi.ac.uk/vol1/ERZ389/ERZ389534/FR07961005.pass.recode.vcf.gz'},
   {'type': 'WGBS Fastq (_1)',
    'download_url': 'ftp.sra.ebi.ac.uk/vol1/fastq/ERR235/002/ERR2359942/ERR2359942_1.fastq.gz'},
   {'type': 'WGBS Fastq (_2)',
    'download_url': 'ftp.sra.ebi.ac.uk/vol1/fastq/ERR235/002/ERR2359942/ERR2359942_2.fastq.gz'},
   {'type': 'WGBS Bam',
    'download_url': 'ftp.sra.ebi.ac.uk/vol1/run/ERR235/ERR2359942/P3255_105_S5_L005.bam'},
   {'type': 'WGBS Bam Index',
    'download_url': 'ftp.sra.ebi.ac.uk/vol1/run/ERR235/ERR2359942/P3255_105_S5_L005.bam.bai'},
   {'type': 'Methylome Report (Released by PGP-UK on 8th March 2018)',
    'download_url': 'https://my.personalgenomes.org.uk/datasets/191/download'},
   {'type': 'Genome Report (Released by PGP-UK on 21 July 2017)',
    'download_url': 'https://my.personalgenomes.org.uk/datasets/79/download'},
...
  'data': [{'type': '23andMe',
    'download_url': 'https://my.personalgenomes.org.uk/user_file/download/103'}]},
 {'hex_id': 'ukB08E17',
  'data': [{'type': '23andMe',
    'download_url': 'https://my.personalgenomes.org.uk/user_file/download/101'}]}]

For example, the first VCF file
ftp.sra.ebi.ac.uk/vol1/ERZ389/ERZ389534/FR07961005.pass.recode.vcf.gz

Am I missing something? Or has the data been moved?

Thanks,
Brian

[IsmailM]

Hi Brian,

Yes, the EBI API has been updated.

I will need to update the scripts accordingly. I will try and get this sorted over the holidays.

[IsmailM]

In the meanwhile, you can access the data directly from EBI depending on the data you are looking for:

https://www.ebi.ac.uk/ena/browser/view/PRJEB17529
https://www.ebi.ac.uk/ena/browser/view/PRJEB13150
https://www.ebi.ac.uk/ena/browser/view/PRJEB25139

On the right, there is an option to switch between Read files (FASTQ/BAMS) and analysis files (VCFs)

[bschilder]

Great, thanks @IsmailM !