Fix URL to GRCh37 Biomart #68
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| @@ -4,7 +4,7 @@ | |||
| import requests | |||
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| LOG = logging.getLogger(__name__) | |||
| BIOMART_37_URL = "https://feb2014.archive.ensembl.org/biomart/martservice?query=" | |||
| BIOMART_37_URL = "https://grch37.ensembl.org/biomart/martservice?query=" | |||
| BIOMART_38_URL = "https://www.ensembl.org/biomart/martservice?query=" | |||
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Should be the same data, right?
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This is a folder with Schug downloads from the beginning of February: 
This the the genes file downloaded today with this branch: 
They're different files! |
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This is a folder from hasta with the Ensembl files I used for updating genes in Scout last time. The same size of the genes files downloaded genes file when the old archive worked. 
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I have now sent an email to the Ensembl helpdesk asking why we see these differences in number of genes downloaded using supposedly the same archive. I think I'll leave this suspended until I get a reply. |
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They did some testing and finally put back online the old Ensembl archive v.75, which seems to be working fine now, so I'm closing this PR and the relative issues in the repo and the ones that use schug as dependency. |
This PR adds | fixes:
How to prepare for test:
sshto ...bash servers/resources/SERVER.scilifelab.se/update-[THIS_TOOL]-stage.sh [THIS-BRANCH-NAME]How to test:
Expected outcome:
Review:
This version is a: